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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

Basic information

species Selaginella moellendorffii
transcript EFJ14420
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os11g06890.1 (Oryza sativa), 3'ss of exon 2
-----------------------------gtaagttcga--tcgatcaaaagccatctttttcttcgatatctccattgat-tggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || | || || |||| || || | ||| | |||| | ||||| | || ||||||| ||||| |||||||| |||||||| || || ||||||||||| ||||| || || || || | || || || |||||||||||||| ||||||||
cctcggtgttcatgactaccctttgtgttgagagcttgaggctactcctaagctgcctactt--tggattacaattctgatatctcttgttggtgttggcagGGCAAATGCACAGCAACCAAAGCTTTTCGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCCCTGTATGGTCTCATTGTGGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
-------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctcca--ttgattggtttgtttttct---------ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| ||| | | | | | || || | | | | || |||| || |||| || |||||||||||| || || || ||||||||||| || ||||||||||| ||||| || || || || | ||||| |||||||||||||| ||||| |||||
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G028432_T01 (Zea mays), 3'ss of exon 1
-----------------------gtaagttcgatcgatcaa--aagccatcttttt---cttcgatatctccattgattggt--ttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| |||| || || | | ||| |||||| || ||||| || | |||||||||| || ||||| || ||||| ||||| || ||||||||||| |||||||| || || || | || |||||||||||||| || || ||||||||
cacttaaacacttgtcctacttgggaaaatcggattgtcaaccgggctggctgcctagacggcgacatctcctcatcctgacacttgttcttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctt--tttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| ||| | | || ||| || || | | | ||| | | || |||||| |||||||| || || |||||||| ||||| ||||||||||| ||||| || || || || | ||||| || ||||| ||||| ||||| |||||
agtagctcacatgcaactttctcctggcgtttcttcttttacagaggaggcatgggaattgaaattttagtttgactaatttttgggccaccgatttcagGGCAAATGCGCAACAGCCAAAGCTTTTCGTTGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTCTATGGTCTAATTGTTGGAATTATCCTT

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | || | || || | || || || | | ||| | || ||||| |||| || ||||| ||||| || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||||| || ||||||||
atgcatttttagttcactcctgttgattatgaattt-actaatagtaatttaagcttcattttgacgaattgaatatgacatgccggtaactcttttgcagAGCAAATGCTCAGCAGCCAAAGCTTTTTGTTGGAATGATACTCATCCTCATTTTTGCTGAGGCGTTGGCATTATACGGTCTCATTGTTGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G04090.1 (Glycine max), 3'ss of exon 2
-------------gtaagttcgatcgatcaaaagccatctt-------tttct--tcga-----tatctcca---ttgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| |||| ||| || | | | | || || || | || || || | |||| ||| | || | ||||| || ||||| ||||| || |||||||||||||||||||| ||||||||||||||||| |||||| | || || || || |||||||| || || ||||||
tgtatattttgctgatagtttgatacatggatataccttttataatgattcctaatagaaattttaccttgaagtttgaacaatttatcttcttatgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTCATTCTCATCTTTGCTGAGGCTCTTGCCCTGTATGGACTCATTGTTGGTATTATCCTG

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | || | || | | || || | | | | ||| | | || ||||| |||| || ||||| ||||| || || ||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||| |||||||| || || ||||||||
acgtcatgttggttcactcctgttgattatgaattt-actaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G07980.1 (Glycine max), 3'ss of exon 1
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttg--tttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | ||| | | | | || | ||| |||| | | | || |||| || || ||||| || || || |||||||||||||| ||||| ||||||||||||||||| ||||| ||||| | || || |||||||| || ||||||||
acgctttgttaaccaagagattgttcaactcttactggatgattgtgtctaacttctattttagttattgaatttgacatgctgaaaatgttttttgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G11760.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | ||| | || || || | || | | | |||| ||| | || | |||| || ||||| ||||| || |||||||||||||||||||| || |||||||| ||||| || ||| | ||||| || ||||||||||| || || ||||||
cattgatggttaattttatacagggatatagtttttataatgatattcctaataaaattcttattttgaagaagt---ttgaacaatttatcttcttccgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTTATTCTCATTTTTGCTGAAGCTCTTGCTCTCTATGGTCTCATTGTTGGTATTATCCTG

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA01G37320.1 (Glycine max), 3'ss of exon 1
---------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
||| | | | ||| | || || | || | ||||| ||||||| || || || ||||| || || || |||||||||||||| ||||| ||||||||||||||||| ||||| ||||| | || || |||||||| || ||||||||
tttttaactgagagattgctcaactcttactggataaatgtgtttaatctcgattttagttattgaatatgacctgctgaaattggactgttttt---tgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G00950.2 (Glycine max), 3'ss of exon 1
------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | | | || | | |||| ||| | | | ||||| | | | | ||||| || ||||| ||||| || || ||||||||||||||||| ||||| ||||| ||||| || ||| | || || || ||||| || || || || ||||||
gaacatatatctttttgcctttactagcatgcatttgttgtgaatttgacggtggattttccttttacaataatactgattaatcaatctgcttctgcagAGCCAATGCACAGCAGCCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCTCTTGCCCTTTATGGTCTAATCGTTGGTATTATCCTG

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA06G00980.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagtt-cgatcgatcaaaagccatctttttcttcgatatctccattgattg-gtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| ||| | || | |||| ||| | | | ||||| || | | | | ||| || ||||| || ||||| || ||||||||||||||||| ||||| ||||| ||||| || || | || || || ||||||||||| || || ||||||
atatatctttttgcctttactagcttgcatttgttgttgtgaatttgacagtggattttccttttacaataatactgattaagtcaatctacttctacagAGCCAATGCACAACAACCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCACTTGCCCTTTATGGTCTCATTGTTGGTATTATCCTG

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G75630.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggttt----gtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| | | | | | | ||| | || || | | || || ||||||| ||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || | || || || ||||||||||| || ||||||||
acaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtt----tgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| | | | | | | ||| | || || | ||| || ||||||| ||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || | || || || ||||||||||| || ||||||||
gtaacgttgtttgatattagatttggtgttggttaagaactgtctggattgaatctttgaagcagattaggataaattaccagtagaattcaacaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------gtaagttcgatcgatcaaaagccatctttt------tcttcgatatctccattgattg-gtttgtttttct-ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
||||||| | | || | |||| | || | | | | | | | || ||||||| | |||||| |||||||| || ||||| ||| | ||||| |||||||| || |||||||||||||| || || | || || |||||||||||||| || ||||||||
atagtcgcagctcctgatattgttgtaagttt--ttgtatggaactcgagttttgaaaggtgttatgtgtttgtaattctggtgtgtgtttttgtgttgcagAGCGAATGCACAACAACCTAAGTTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCTGAAGCACTTGCCCTGTACGGTCTCATTGTTGGTATCATCCTC

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtaagttcgatcgatcaaaagccatctttttcttcg-atatct--ccattgattggtt---tgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|||||| | | | | | | ||| || | | || ||| ||| | || ||| |||||||||| ||||||||||| || || ||||||||||| ||||||||||||||||||||||| || || |||| |||||||| || ||||| || || ||| ||
gactgtactttggacgactttaggataagttgctttggctgaggacaaattctttgttagtaggactaatcataatttgaatctatgatttgttttgcagGGCTAATGCGCAGCAGCCTAAACTTTTTGTTGGTATGATCCTCATTCTCATCTTTGCTGAAGCACTGGCCCTATACGGCCTTATTGTTGGCATTATCTTG

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtaagttcg-atcgatcaaaagccatctttttcttcga----tatctccattgattggtttgtttttc--tttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| || || | || | |||| | | ||| | ||| || ||||| || ||||||| || ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| || ||| | || || || || || ||||| || ||||||||
tttcatattaggatttctgcctttgcctttttacatctattcaattctatttatttcctttaagagtatgttt-ttgtctgaattgttgttatatttgcagAGCCAATGCTCAGCAGCCAAAGCTTTTCGTTGGAATGATCCTCATTCTCATCTTTGCTGAAGCTCTTGCCCTGTATGGACTTATTGTTGGCATCATCCTA

upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gtaagttcgatcgat-caaaagccatctttttcttcgat---atctccattgatt---ggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| | || ||| | | || || | ||| || || | | | || || | |||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || || |||||||| ||||| ||||||| || || ||||| ||||| |||
gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG

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|169036531|gb|FE444115.1|FE444115
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST: gi|169051425|gb|FE457697.1|FE457697
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST: gi|169051424|gb|FE457696.1|FE457696
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST: gi|70669212|gb|DN837789.1|DN837789
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT

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: 34 (upstream exon), 35 (downstream exon)
Score: 91

TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
                            cattgat  putative branch site (score: 91)
 tttgtttttctttgc  putative PPT
 tttgttttt  TA-rich tract