Sequence
atgc intronic sequence ATGC exonic sequence...cataatccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S52_57V6.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
-cataatcc---atttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
| | || || || |||| ||| || | | |||| | | ||| | | || || | ||| | || ||||||| || |||||||||||| |||| ||||| || ||||| |||||||||||||| | || ||||| ||||| |||
ttacagtcttgtatgtctgatactctgatgcctcaaacgtttgtacggattgtatgc-tgagagtgaccattttcaactgactgatgttcgtg---ctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
cataa-tccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgt--gtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
|||| | ||| | | | | ||| ||| | | || || || | | || | | |||| || ||| | || | |||||||||| || || |||||||||||||| |||||||| |||||||| |||||||| || | |||||||| ||||| |||
-ataaattcatggttatttgataggttt-gatggattgagcattctcgata-aattaataggcatagtggttgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
cataatccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtg---tgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
|||| | | || | ||| ||| | | || || || | | || | |||| || ||| || || | |||||||||| || || |||||||||||||| |||||||| |||||||| |||||||| || | |||||||| ||||| |||
-ataaatttatgcttgtttgataggattgatggattgagcattctcgata-aattaataggcattgtggttgggtcaaatgttaattgtttcat-tcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
--------------------------------------------------------------cataatccatttcaacc-tttctgttgcagatctatttaagagaaacggtata--aattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
| ||| || ||| |||| | ||| | | || | || ||| || | | | ||| | | || |||| | | ||||| || || ||||||||| | |||||||||||||||||||| |||||||| | || || || || |||||||||
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttga-attatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
-------------------------------------------------cataatccatttcaacc---tttctgttgcagatctatttaagaga-----aacggtataaattttcgggacattg----gtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
||| | | | || || ||||| | || | | || || | || | | ||| || | | || ||| | | | ||||| || || ||||||||| | || ||||||||||||||||| |||||||| ||| || || ||||| || |||
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtcatg-actttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtataaattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
gcttgac putative branch site (score: 4)
taaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataatccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - -tgttgca