Sequence
atgc intronic sequence ATGC exonic sequencegtacaacatatcacaattaatgtttaactctcgaaatctctaatcataatgcttaaagtggatttatcattaatgtgtaatttgcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G104074_T01 (Zea mays), 3'ss of exon 3
---gtacaacatatcacaattaatgtttaactctcgaa---atctctaatcataatgcttaaagtg-gatttatcattaatg-tgtaatttgcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA----
| | | | | ||| | ||| || | |||| | | || || | | | | ||| | |||| ||||||||||||| ||||| ||||| || || |||||||||||||| || || ||| |||| | |||| | | | ||
gtaacaagctagaggccttgtgttgtacacttctttaatttgtttctactagcagctggcaagttgtaaagcaactctgatgatctaatctgcagGAAGATGGATGGGTGGTATGTAGGGTTTTCAAGAAGAAGAACTATGAGCAGAGAGGCCAC----AACATGGCTGAGATGGCGGCACTGGACGACGATGAGCTCC
upper sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 3
----------gtacaacatatcacaatt--aatgtttaactctcgaaatct---ctaatcataatgcttaaagtggatttatcattaatgtgtaatttgcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA-
||| | || || | |||| ||| | || ||| |||| | ||| | | | | | ||||| ||| |||||||||||||||| |||||||| |||||||| ||||| | || | |||| || || |||||| || |||| | || | | |||| |||
ctgtatgactgtatatcacat-ataattcaaataatgggtcctgtggatccaacttaatagccagatataatgacaaagtgttctcg-tgtgtttcttgtagGAAGATGGGTGGGTGGTATGCAGGGTGTTCAAAAAGAAAAGCCAAAACCGAGGTTTCCAGCAAGAAATTGAAGAAGAAGAGCACT-TAACCACCCATATGA
upper sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 4
-gtacaacat--atcacaattaatgt--ttaactctcgaaatctctaatcataatgcttaaa----gtggatttatcatta-atgtgtaattt---gcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA-
|| || | |||||| || | |||| |||| | | | |||| | | | | | | | | ||| |||||| |||||||||||||||||| |||||||| || ||||| ||||| || || | |||| || || ||||||| || |||| | || | | |||| | |
catatcactttaatcacatatagttcaaataacactcgtacggatccaacttaatttccagataatgacaaagtgttttcatgtgtttaatttcttgcagGAAGATGGGTGGGTGGTATGCAGGGTCTTCAAAAAGAAAAACCAAAGCCGAGGTTTCCAACAAGAACTTGAAGAAGAAGAGCACT-TAACCACCCACATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatctctaatcataatgcttaaagtggatttatcattaatgtgtaatttgcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA
cattaat putative branch site (score: 3)
atttatcattaatgtg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaacatatcacaattaatgtttaactctcgaaatctctaatcataatgcttaaagtggatttatcattaatgtgtaatttgcagGAAGATGGGTGGGTTGTATGCAGAGTGTTCAAGAAGAAGAATCATTTCAGAGGATTTCACCAAGAACAAGAGCAAGATCATCATCATCATCACCAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA