Sequence
atgc intronic sequence ATGC exonic sequence...cttttaaatattaaatgcagcaatgcttactcgtcttgttttcctcaatccatgatgaaattgtgcatcagttattgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S51_296V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
cttttaaatattaaatgcagcaatgcttac----tcgtcttgttttcctcaatccatgatgaaattgtgcatcagtta-ttgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG
| | ||| || || | || | || | | | | | | | | ||| | ||| | | | |||| | ||| ||| | |||||||||||| |||| | ||||| ||||||||| | ||||| |||||| ||||||| |||||||||| ||| || || | || | | |||
-gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactgttctataatagcttgacttatttaatattcgc----agTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
upper sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 7
--cttttaaatattaaatgca-gcaatgcttactcgtcttgttttcctcaatccatgatgaaattgtgcatcagtta-ttgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG
| | ||| || || | ||| | || | | | | | | | | ||| | | | | | || |||| | ||| || | |||||||||||| |||| ||||| ||||||||| | ||||| |||||| ||||||| |||||||||| ||| || || | || | | |||
tgtgatgaggggttagattcacactttgcaaagtccccctttcatgcatactgttggttgagactttcctataattgcttgacttatttaatatccgc----agTTGGAGAAAAGTGCAGCACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatccatgatgaaattgtgcatcagttattgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG
aaataac putative branch site (score: 2)
atcagttattgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttaaatattaaatgcagcaatgcttactcgtcttgttttcctcaatccatgatgaaattgtgcatcagttattgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG
- - - - - - - -tgcagca