Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtttcaataagcctttcatctcctgactggtccttacagaaagtgtgtccatcttcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG
Basic information
species | Physcomitrella patens |
transcript | PP1S79_95V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 10
gtgtgtttcaataagcctttcatctcctgactggtccttacagaaagtgtgtccatcttcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG-----------------
||| ||| ||| ||||| || || || || || | || || | | |||||||| ||||||||||| ||||| ||| | ||||| | |||||| |||||||| | || |||||||| |||||||| ||||||||||| || ||||
--------------------------------------------------aaatgccttaaattcttc---tgtctc-tgtgacatttgacgtggtatat-actttaatacagattccattttgtgttgttattggttggacgatgggacaaaagATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG
upper sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 10
gtgtgtttcaataagcctttcatctcctgactggtccttacagaaagtgtgtccatcttcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG
| ||| | | | | | | |||| ||||| ||| || ||| ||| ||| ||||| || || || || || | || || | | |||||||| ||||||||||| ||||| ||| | ||||| | |||||| |||||||| | || |||||||| |||||||| ||||||||||| || ||||
tttagttgtcaaggacacataagtacattactgaa--ttacataaaatgc------cttaaattcttc---tgtctc-tgtgacatttgacgtggtatat-actttaatacagATTCCATTTTGTGTTGTTATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGG
upper sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 9
gtgtgtttcaataagcctttcatctcctgactggtccttacagaaagtgtgtccatcttcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG
||| | | | || | | | |||| ||| ||| | || ||| | || | || | || || || | | | | | ||||||||| ||||||||||| ||||| ||| ||||| |||||| |||||||| | || |||||||| |||||||| ||||||||||| || ||||
---aattttagtca----ttgaggaaccagaagtcaattactgaattacataaaatccttaaattcttctacctc---cgtgacgtttggcatggtatactccaat---gcagATTCCATTTTGTGTTGTTATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG
aattaac putative branch site (score: 2)
aattaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtttcaataagcctttcatctcctgactggtccttacagaaagtgtgtccatcttcaatcctttcaatgtctagcatggcaattaacacggcacattgctgttgtgcagATTCCTTTTTGTGTTGTCATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG