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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

Basic information

species Physcomitrella patens
transcript PP1S200_79V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
-cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcg-acttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| || || | | | || || || | | | | |||| | ||| | |||| ||| | | ||| | |||||||||| || || || ||||| || ||| || || || ||||| |||||| ||||||||||| |||||||||||||||||||||||||| |||||
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaat-ttggttataattttg-cagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os05g01560.1 (Oryza sativa), 3'ss of exon 1
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| || | || |||| ||| || ||| | | || || |||| | | | | | |||||||||||| || || || || |||||||| || ||||| ||||| |||||||| |||||||| || || |||||||||||||| ||||| || || ||
-------------gtaagctcccaatcttccccttcactttctcggggccagatctga-----tctgagatgaggttgacacacgacgc----atgcaagGCATGGGCGCCGCCTACGGCACCGCCAAGAGCGGCGTGGGCGTGGCGTCCATGGGGGTGATGCGCCCGGAACTGGTGATGAAGTCCATCGTCCCCGTCGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os11g06890.2 (Oryza sativa), 3'ss of exon 1
----cccgtgaacgg---tgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| || ||| ||| ||| | ||| | | | | | || | | | | || | | || || | |||| ||||||||| || || || ||||| || ||||| || || || ||||| |||||||| |||||||| || ||||| ||||||||||| |||||||| |||||
ccgattggagatcggatttgtggggaaaaaaagttgggagctttggattctgttcttgatggggggatttgcttatttgctttca---ttcgat-ctgttgc---agGCATGGGTGCGGCGTACGGGACGGCGAAGAGCGGCGTCGGCGTGGCGTCCATGGGCGTGATGCGCCCGGAGCTCGTGATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G101020_T01 (Zea mays), 3'ss of exon 1
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagg--gtgcgacttcgaaactcctggacatgaactaaatg------ttgaatgttattgcgt------cagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | || | || || ||| || ||| || ||||| | ||| |||| | ||| | ||| || || |||||||||| || || || ||||||||||||||||| || || ||||| ||||||||||| ||||| || ||||| || |||||||| |||||||| |||||
--------------gagagaatttgggttggatccatgtggctgggacgtgtgagggcgaaatttttggtggtgaatgacatgatctccctctgtgtatgtgtgtggctcgcagGCATGGGGGCGGCGTACGGGACAGCCAAGAGTGGCGTCGGCGTGGCGTCCATGGGTGTCATGCGCCCAGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 1
-----cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| ||| |||| | | || | ||| | | | | | ||||| | | | | ||| || | | ||||||||||||| || || ||||| || ||||| || || || ||||| || ||||||||||||||||| ||||| || |||||||| |||||||| |||||
gatttggtccgatcgggtgtgggatttcagaaatcgacagccttttcccgt---cagacaggcaggtcctgactacgctgttctt-ttgcttgatccgatg-cagGCATGGGCGCAGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 1
-cccgtgaacgg-tgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| ||| ||| | | | | || | | | || | | | ||| | | | | | ||| || | ||| ||||||||||||| || || ||||| || ||||| || || || ||||| || ||||||||||||||||| ||||| || |||||||| |||||||| |||||
tggtccgatcgggtgtcagtctgtcggattccagaaagcggtgggctttttcggtcgggcagttgctgactaggctgttatt-ttgcttgatccggcg-cagGCATGGGCGCCGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM5G893252_T01 (Zea mays), 3'ss of exon 1
-------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
||| | | | | | | || || | || | | || | || || | | | | | || | | ||| | |||||||||||| || || ||||| |||||||| || || || || || |||||||| || ||||| |||||||| || |||||||| ||||| || || ||
gtaagcacccatca--gatctccctccctcccttctctgtctctttcaccag----ccggatccaaccatccattcctcactcccatcacctcggctggtgcct-agGCATGGGCGCCGCCTACGGGACGGCCAAGAGCGGCGTCGGCGTCGCCTCCATGGGCGTCATGCGCCCCGAGCTCGTCATGAAGTCCATCGTCCCCGTCGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA06G00980.1 (Glycine max), 3'ss of exon 1
---------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| ||||| | ||| | | | || ||| | |||||| | || | | | || | || || || ||| ||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||| ||| | || |||||||||||||||||||| || ||||| ||
aatttcacacgtgtgaaagtgattgatcgatcgaattttaatct-------tagggttgtttgtttgaattgataaaaatttgtgaggaattttattttgttga--tagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCCATGGGTGTAATGAGACCTGAGCTGGTGATGAAGTCGATTGTTCCTGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA04G00950.1 (Glycine max), 3'ss of exon 1
----cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgc-gtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| ||||| | ||| | | | | ||| | | | | | || ||| || ||| | || | | | | || | ||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||||||| | || ||||||||||||||||| || || ||||| ||
cactcatgtgaaagtgattgatcgatcgaatcttaatct--tagggttgtttgaagtgataaaatctgtgag---gaatttcatttgtatttgaactgttgatagGTATGGGAGCTGCCTATGGCACAGCAAAGAGTGGTGTGGGCGTGGCTTCCATGGGTGTGATGAGACCTGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA14G23990.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------------------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | | | ||| |||| || | || | || | | | | | || || || || | | | |||| ||| ||||| || || || || || || |||||||| ||||| ||||| || ||||| |||||| |||| |||||||||||||||||||||||||| |||||
gttcgccactctctctatctctctctttttgtttataattttttatttaatttaacgataacaacaatactactaataataataccaagctctagcgtgagttattgaaaactttctgttatctgtctttgttacggattaaaaaaatatgatttattccgtggcctttatttttattatgattgg--tagGTATGGGAGCGGCGTACGGAACGGCAAAGAGTGGGGTGGGGGTGGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G03470.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------cccgtgaacggtg-ttgggcacttaagcttcaa--tttcctcagctagggtgcgacttcgaaactcctggacatgaacta-------aatgttgaatgttattgc-gtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | || ||| || ||| | || || | | | | ||| | | | | | |||| || |||| || |||| | ||| ||||| || || ||||| || || |||||||| ||||| ||||| || ||||| |||||| |||| |||||||||||||||||||||||||| |||||
gttcgtcactctctttttatttgtaaaattttattcaatataacgataacaataataataataatattagggtctagatctatcgtagttggttgaacagttattgtaaaaacctttttgtacctgtcttcgattgctacagattaaaaaatgatttattctgtggctgttttattttatgattggtagGTATGGGAGCGGCGTATGGAACGGCGAAGAGTGGGGTGGGGGTGGCGTCGATGGGAGTGATGAGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G04090.1 (Glycine max), 3'ss of exon 1
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggt-gcgacttcgaaactcctggacatga-actaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| | | | | || | | | || | ||| | || ||| | | | | | || |||| | | || | | ||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||| || |||||||||||| | || ||||||||||||||||| || || ||||| ||
--tgtatataaagaaagaaaaagaaattctgagcttcttcgatagctttgcattttctgtagatttatctttaatatgaattgtttgaactgatggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGATGGGTGTGATGAGACCGGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G11760.1 (Glycine max), 3'ss of exon 1
-----cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | | | || || | | | || | ||| | | || | || | | ||| | | || || | ||| ||||| ||||| ||||| ||||| |||||||| || || ||||| || |||||||||||| | || ||||||||||||||||| || || ||||| ||
ttatgcgtatatataaagaaagacaaagaaattcagagcttcttcgttagctttgcattttt---tctgtagatttatctttaatactaattg--atggatgaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTTGGCGTGGCTTCGATGGGTGTGATGAGACCAGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 1
cccgtgaacggt--gttgggcacttaagcttcaatttcctcagctagggtg--cgacttcgaaactcctggacatgaa-ctaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| | | || || ||| | || | ||| || | | |||| | ||| | | || || ||||| ||||| || || || || || || ||||| || || || || || || ||||| |||||| |||| |||||||||||||| ||||||||||| || ||
---gtaactaactcatcaaatcaaagagtttttttttttttttttacaatttccgaaaccggcgtcgttttatctgaaaccgtgtgtcgttt-ttgttttttcagGTATGGGAGCGGCGTACGGAACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
----cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| ||| | || || || |||| | | | ||| | | | ||| ||| | | || || ||||| |||||||| || || || || || ||||| || || || || || || ||||| |||||| |||| |||||||||||||| ||||||||||| || ||
gtaactaactaact-catcaaatcaaagagttttttttgtctcatttcccgaa-accgtcgtcgtttt--atcttaaaccgtgtgtcgttt-ttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
-------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | | | | | | | || | | | | || || | || | | || | | ||||||| ||| ||||| ||||| || |||||||| |||||||| |||||||||||||| |||||||||||| |||| ||| ||||||||||||| || || || || ||
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatc------tttgtgttatta-acaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaa-atgttg--aatg--ttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | | || | | | | |||| | || || | || || | | || | | |||||| | || || | | | ||| ||||| ||||||||||| ||||| |||||||| || || ||||| || ||||| |||||| | || ||| |||| |||||||| || || ||||||||
---attagtgttcttag--atcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 1
cccgtgaacggtgttgggcacttaagcttcaatttcctcagcta--gggtgcgacttcgaaactcctggacatgaactaaatgttgaatgt-tattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | | | ||| ||||| ||| |||| | || | | || | || | | | ||||| | | || | | ||| ||||| ||||| ||||| || || |||||||| || |||||||| || ||||| |||||| |||| |||||||||||||||||||| || || || ||
--attcgataatttcttctccttcttcttca-ttttctcaataaccggacatagatatatagatcttcgattctgattgactgttgtttttataatttttgagGTATGGGAGCTGCGTATGGAACGGCGAAGAGTGGCGTCGGAGTGGCGTCGATGGGAGTGATGAGGCCGGAGCTGGTGATGAAGTCGATTGTACCAGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv18s0001g02650.t01 (Vitis vinifera), 3'ss of exon 1
-cccgtgaa---cggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
|| ||| |||||| | | || | || || | | | | | | || | | | | |||| | ||||||||||||| || |||||||| || ||||| || ||||| ||||| |||||||| |||||||| || ||||| || ||||| ||||| || || || ||
tccgacgaaacaaagtgttgtattttcccacatcggaactgtttcctgtggaaacaaatggggctttttt--cttggaatg--tttctaatggcttctttacagGCATGGGCGCGGCCTATGGGACTGCAAAGAGCGGGGTGGGTGTGGCCTCCATGGGAGTGATGCGACCGGAGCTCGTCATGAAATCGATTGTCCCAGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 3'ss of exon 1
-cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcct-ggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| | ||| | | | | | || | | | || | | | || | || || | || || || || ||||| ||||| ||||| ||||| || || ||||| || || || ||||| ||||||||||||||| | || ||||| || |||||||||||||| || || ||
tctcagcaaccaaaccgag-gttaatgtccgtccgtcttgggtttggatttggatctagggcttttcaaacgtggatctgattttttat-ttgggatctcagGTATGGGAGCTGCATATGGAACCGCAAAGAGCGGGGTTGGTGTGGCCTCCATGGGTGTGATGAGACCGGAGCTTGTTATGAAGTCGATCGTTCCAGTTGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctag------ggtgcgacttcgaaactcctggacatgaacta---aatgttgaatgttattgcgt---cagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| || | |||||| | | ||| ||||| || | | | | ||| | | | | || | | | | ||| ||| | |||||||||| ||||| ||||| || || |||||||| || ||||||||||||||||| ||||||||||| ||||| |||||||| ||||||||||| |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatgga--ttcgccttcctgcgcgatttccttgccacaatcccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctag------ggtgcgacttcgaaactcctggacatgaacta---aatgttgaatgttattgcgt---cagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
| || | |||||| | | ||| ||||| || | | | | ||| | | | | || | | | | ||| ||| | |||||||||| ||||| ||||| || || |||||||| || |||||||| |||||||| ||||||||||| ||||| |||||||| ||||||||||| |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatgga--ttcgccttcctgcgcgatttccttgccacaatcccgatatttcgatcccaaaattccccattttctcatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCGTCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162275184|gb|FC451771.1|FC451771
EST:     TGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: TGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67703023|gb|BJ963256.1|BJ963256
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162207190|gb|FC382512.1|FC382512
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162212908|gb|FC388916.1|FC388916
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67709770|gb|BJ965586.1|BJ965586
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67723846|gb|BJ974105.1|BJ974105
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162275185|gb|FC451772.1|FC451772
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162207189|gb|FC382511.1|FC382511
EST:     GGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: GGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162262065|gb|FC437886.1|FC437886
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162262064|gb|FC437885.1|FC437885
EST:     GGCTTCATGGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: GGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67703810|gb|BJ964043.1|BJ964043
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|19783928|gb|BQ040091.1|BQ040091
EST:     CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCAT                         GCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 29 (upstream exon), 29 (downstream exon)
Score: 2

ATTAATACCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCCCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTTTCATgtatggactc ... attgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT
                           aactaaa  putative branch site (score: 2)
 aatgttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa