Sequence
atgc intronic sequence ATGC exonic sequence...tttactccctcctgttccctttggtcagtaatttttaaatgtcgttagcggactgtgaagatgagttcaaggtgccaacgatattggatttaatacgcagACCCGGAAGCCGAGGTGATAGCTTTATCACCAAAGACATTGATGGCCACGAATCGATTCGTGTGCGAAATTTGTAACAAGGGGTTTCAGCGAGATCAAAA
Basic information
species | Physcomitrella patens |
transcript | PP1S63_51V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S63_51V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA01G38290.1 (Glycine max), 3'ss of exon 1
tttactccctcctgttccctttggtcagtaatttttaaat--gtcgttagcggactgtgaagatgagttcaaggtgccaacgatattggatttaatacgcagACCCGGAAGCCGAGGTGATAGCTTTATCACCAAAGACATTGATGGCCACGAATCGATTCGTGTGCGAAATTTGTAACAAGGGGTTTCAGCGAGATCAAAA
| | | ||||| ||| || | | | |||| | | | | | | ||| || || | |||| ||||| || |||||||| ||| | || || ||||| ||||||||||||| || |||||||| |||||||| ||||||||||||||| | || || ||
----------gtaccacaaaaaaattcattttttttcaatcaatcatcatcatcttgtgttgtttttcttattttactttt--tatggggtt----attcagATCCGGATGCAGAGGTGATTGCTCTGTCTCCGAAGACCCTGATGGCCACGAACCGTTTCGTGTGTGAAATTTGCAACAAGGGGTTTCAGAGGGACCAGAA
upper sequence: PP1S63_51V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT5G66730.1 (Arabidopsis thaliana), 3'ss of exon 1
tttactccctcctgttccctttggtcagtaatttttaaatgtcgttagcggactgtgaagatg---agttcaaggtgccaacgatattggatttaatacgcagACCCGGAAGCCGAGGTGATAGCTTTATCACCAAAGACATTGATGGCCACGAATCGATTCGTGTGCGAAATTTGTAACAAGGGGTTTCAGCGAGATCAAAA
||| | || | ||||| | ||| || | |||| | || || || | | | | | ||| | ||| || || || || ||||||||||| ||||| || ||| | ||||| |||||||||||||| |||||||| |||||||| || ||||| || || || ||
----------gtacttctcaaaaatccaaacttttttttttctgttttttgagtttgaaattttctgtttttagttgttctcactgattgtctaaattc--agATCCAGACGCTGAAGTGATAGCTTTGTCACCTAAAACACTTATGGCAACGAATCGATTCGTTTGCGAAATCTGTAACAAAGGTTTTCAACGTGACCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcggactgtgaagatgagttcaaggtgccaacgatattggatttaatacgcagACCCGGAAGCCGAGGTGATAGCTTTATCACCAAAGACATTGATGGCCACGAATCGATTCGTGTGCGAAATTTGTAACAAGGGGTTTCAGCGAGATCAAAA
atttaat putative branch site (score: 4)
atattggatttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttactccctcctgttccctttggtcagtaatttttaaatgtcgttagcggactgtgaagatgagttcaaggtgccaacgatattggatttaatacgcagACCCGGAAGCCGAGGTGATAGCTTTATCACCAAAGACATTGATGGCCACGAATCGATTCGTGTGCGAAATTTGTAACAAGGGGTTTCAGCGAGATCAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA