Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcacctacaattgcagatagtctctcttttaacacaaaatcccggatgcaataaactaatgtgtcgacttctgaatcagTTATATGTTTAAGCTTCTGGGCTGAGGTTCATTACAATTCAATCTACCCTGAAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04250.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04250.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S31_91V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------gtaagtcacctacaattgcagatagtctct------cttttaacacaaaatcccggatgcaataaactaatgtgtcgacttctg------aatcagTTATATGTTTAAGCTTCTGGGCTGAGGTTCATTACAATTCAATCTACCCTGAAGGAG
|| || || | | | |||| | || ||| || || | | |||| | | | |||| | | ||| || | | |||||||||||||||| |||||||||||||||||||| ||| |||||
gtcttgcttcttcccatgcagccctgcaaagtgtgatttgaccaaatcaaagtatttataacatttaaactctgcggctgtctttatcagcctacaaactcataacatctcctctgataaggttctcctttgactgtggttgtccatgcagAGATCTATCTAAGCTTCTGGGCTGAAGTTCATTACAATTCAATCTATTCTGTAGGAG
upper sequence: AT5G04250.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S431_23V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------gtaagtcacctacaattgcagatagtctctcttttaacacaaaatcccggatgcaataaactaat-------gtgtcgacttctgaat-------------cagTTATATGTTTAAGCTTCTGGGCTGAGGTTCATTACAATTCAATCTACCCTGAAGGAG
| | | | || | ||| || || | || |||| || | | || | |||| | || | | ||| |||| |||||||||||||||||| | |||||||| |||||||| |||| |||
gtctcatttcctaccatccagccgtctacagtgtgtcatttgaccaggatgaacttattccgtatgttctaactctgtcgttgtgctcataatcttagaaacctacagcttctctgactagtgtttattttgggacgtggtcgtgtatgcagAGATATATTTAAGCTTCTGGGCTGAAATCCATTACAACTCAATCTATCCTGTGGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttaacacaaaatcccggatgcaataaactaatgtgtcgacttctgaatcagTTATATGTTTAAGCTTCTGGGCTGAGGTTCATTACAATTCAATCTACCCTGAAGGAG
aactaat putative branch site (score: 2)
cttct putative PPT
aataaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcacctacaattgcagatagtctctcttttaacacaaaatcccggatgcaataaactaatgtgtcgacttctgaatcagTTATATGTTTAAGCTTCTGGGCTGAGGTTCATTACAATTCAATCTACCCTGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG