Sequence
atgc intronic sequence ATGC exonic sequencegtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S83_25V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 10
gtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatga-gtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA
|||||| || | || ||| | | || || | || | ||||| || | || | || || | || | | |||| ||||| |||||||| || || |||||||||||||||||||| ||| | | || ||||||| | ||||| || | || | |||||
----gtattctaaagtttcgaggcaatagtt---------cataatgcatctgatcct-gttatatcatctataact-gatagaataaccatgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 12
-----------------------gtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA--
||| | || | | || | | ||| | | | | ||| | | | || | | ||| | | | ||||||| || || ||||| ||||| || ||||| |||||||||||||||||| | | ||||| | | | || || ||| | | | | |||
gtattggcatgttcagggacactgtactcttcctagttcttaatttcgacctttggacttgactcatatcttcattactttgaagttattttattttattggtattttatcattctttga-agGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGACGTAATGTTGCGACGCTATTCCAAAGCTCG--ATCTGCTGTGGGTGAATCTTTGAATGAAG
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA
| | || || | | | | | || | |||| ||||||| | | || |||| | | | ||||||| || || ||||| ||| ||||||||||||||||||| || |||||| | | || || | | | || || ||||| | || | |
-------gtttaaacatcactatttgtg----gatcattatattatgaagc-aattcc--ttatgagatattcaatttgggtaacttgtatgtttg-tagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA
atttaat putative branch site (score: 4)
tcccttt putative PPT
aacaatttaatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC