Sequence
atgc intronic sequence ATGC exonic sequence...tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
Basic information
species | Physcomitrella patens |
transcript | PP1S147_62V6.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 3'ss of exon 6
--------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgt-----aggctcatccacgtaatcgct-----tcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
||| | | | | || | | | | | | | | | | ||| || || || | | | | | | | || | || ||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||| |||| || || || || || || ||||| | ||| || |||
gtgagacattaaagcatttggtttcacattatctttgttgcttctctcctctcttatagttgttattctctttttttggggctctacaacaagtgcggcactaaagtttctcatttttgtatagGTATTTCTCATATGAGCATTTTTATGTGATATATTGCAAGTTCTGGGAGCTGGACACAGACCATGATTTCTTCATTGATAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
tattggcatgccctcaatagaag--acagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaat--cgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| || | | || ||| | | ||| || | | || || ||| | | | | | | | | | | || | ||||| ||||||||||| || || |||||||| ||||| |||||||| |||||| |||| ||||||| || |||||||| || ||||| ||||| | |||||
---acgaattacttggattcaagttatattatt-tatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G104254_T02 (Zea mays), 3'ss of exon 3
-tattggcatgccctca-atagaagacagtatggtacattgat-gtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| ||| ||| | | ||| || | || || | | | ||| | || | ||| ||| | ||||| |||||||||||||| || |||||||| || |||||||||||||||||||||||| |||| ||||| |||||||| || || || |||| | ||||
cggattacatttgttcacgctgttttctttatatagtcttaacagtattctttgtataatgtttgccaaattgataatcttggctcgtgatc---tgatgcagATACTTCTCATATGAGCACTTTTATGTGATCTATTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAGAACCTCATCAAATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtat-----ctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|| | | || ||| | || || || | | | || | || ||||||| | | | | | | | | |||||| || |||||||||||||| |||||||| || || ||||||||||||||||||||| |||| ||||| |||||||| || || || | || | ||||
---ccatttgttttgtgtggattacattt--gttcactgttttctttatatagtcttaactgtgtataacgtttactgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G040094_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctact-tgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|||| || || | | |||| | | | || | | || || | | || | | || || | | | || || |||||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| |||| |||||||| || || |||||||| | ||| || |||
gtgacaccttcaaatcaagtcctaacaattcccttcctttgtatttacaaaatttc--tcaagtgcagttt--ttctttaggggaaccctaaactttcattatgcaacacattgaacttattgt--ttgttttcccctgtagATACTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAACTGGACACAGACCACGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 6
-------------------------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| | || | | | |||| | | | | ||| | || | ||| | || || | | | | || | | | | || ||||| ||||||||||| ||||| ||||| ||||||||||| |||||||||||||| | ||||| ||||| || || |||||||| | ||| || |||
gtgacaccttcaaatcatgttctaacagttctgctcctttgtattttctcaagtgcagttt--ttcttcaatggaaccctaagcttcca-ttatgcaacacactgaacttcttgtttgtgtttccctgtagGTATTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAGCTGGACACCGATCATGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
-------tattggcat-gccctcaatagaagacagt-atggtacattgatgtgaatttaggtttctacttgtgtatct---gtaggctca-tccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|| | ||| | | || | ||| | | | || | || || || ||| | | | || | | | || |||| | || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| |||||||||| || || ||||||||||| | ||| | |||||
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
-------tattggcatgccctcaatagaagacagt-atggtacattgatgtgaatttaggtttctacttgtgtat-ctgtaggctca-tccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|| | | | | || | ||| | | | || | || || || || | ||| | | | ||| |||| | || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| |||||||||| || || ||||||||||| | ||| | |||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
--------------------tattggcat-gccctcaatagaagacagtatggta--cattgatgtgaatt---taggtttctacttgtgtatctgtaggctcatccacgt-----aatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
||| || | ||| | | ||| | || ||| | |||| | || ||| || | | || || || | || | | | | |||||||||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||| || || |||||||||||||| | || | |||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgcct-taatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
--------------------tattggcat-gccctcaatagaagac---agtatggtacattgatgtgaatt---taggtttctacttgtgtatctgtaggctcatccacgt-----aatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
||| || | ||| | | ||| || | | ||| | ||| | || ||| || | | || || || | || | || | |||||||||||||| || || ||||||||||| ||||| ||||| || |||||||||||| ||||||| || || |||||||||||||| | || | |||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcat-tattcaaacgaactaaatatatttgtattatgatgcct-taatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 7
----tattggcatgccctcaatag-aagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| || | ||| | || ||| | | || |||| || || | | | ||| || | | | | | | | | |||||||||||||||||| |||||||||||||| || |||||||| |||||||| || ||||||| |||||||| || || | ||| ||||| || ||||
aaattcatgattgactttcattttcaatttagttctctctgtagaattgaaatt---ttcttgtctttttatttgcttcattaattatcttacggaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
----tattggcatgccctcaatag-aagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|| | ||| | || ||| | | || |||| || || | | ||||| || | | | | | | | |||||||||||||||||| |||||||||||||| || |||||||| |||||||| || ||||||| |||||||| || || | ||| ||||| || ||||
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaatt---ttcttgtctttgtatttgcttcattaattatcttacgaaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgta--ggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| || | | || | | || |||| ||| || | | || | || || | | || || || || | | || |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||| | |||||||| || |||| |||||||| | ||| | |||||
---------gtact-gacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt-tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
|||| | | || | |||| | |||| || ||| | | | | || || ||| || || | | | ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||| ||||| ||||||| || || || || |||||||| | || | ||||||
-gttggtgtcttaagattaattagtaatatg--aaattggtgcttattaacggcttttatta---------agactc-tctac-tgtttatt------agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcg---tgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| || | | || | | | |||| ||| ||||| | | || || | || ||| || || ||| | || |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||| | |||||||| || |||| |||||||| | ||| | ||||||
---------gtactgacaaaaatatt-tgcgtgctattgttgt--atttatagtattgtttttgctcatttaacatcacttttctattcactttggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
--tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcg--tgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| | | | | | || | | ||| | | | ||| | | || || ||||| | || || || |||| ||||||||||| || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||||| || || ||||| |||||||| | || | |||||
aacaacagagagacacatgcatatatttgttttat-tattagattaactagttatttatgatgatgaattgctaggccc---catgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 4
----tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
| | || || | |||| | | || | | || |||| ||| || || | || | | | | || | ||| ||||||||||| |||||||| || ||||| ||||| ||||| ||||||||||||||| | || || || |||||||| || ||||| |||| | |||||
tatttgtgggaatactctcataacatttt--tagcatgtactg-tgtggtattaaaattttaacaccattgcttttttttttttgat-tatgcccttaccatagGTACTTCTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGATACCGACCATGATTTTTTGATTGATAAAGAGAACCTAATCAGATATMapped 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|162193203|gb|FC369963.1|FC369963EST: ACTGCTCTTCAGCAAGTGGATGAAGAAGAAGATATCAACAAAGTGTTGCG GTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCT
genomic: ACTGCTCTTCAGCAAGTGGATGAAGAAGAAGATATCAACAAAGTGTTGCGgtgagtatat ... cttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
tcgcttc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG