Sequence
atgc intronic sequence ATGC exonic sequence...ccggatcccctcaaatttgccatgactgccattttgtagcttgattgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 2
------ccggatcccctcaaatttgccatgactgccattttgtagcttgattgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
| | | | || || || |||| | | || || || | || | ||| || | | | | ||| ||||||| |||||||| ||||||||||| |||||||| || ||||| || || ||||||
taaacaggaaagcaatttattccagctttggttgacattgt----tctcatatatgtcttgagtt--ttttattatggtgactcttattccaattaatattttcagGTAAGGATGTCCTTGCCAAGGCCAAGACAGGCACCGGAAAAACAGTAGCCTTTTTG
upper sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 2
ccggatcccctcaaatttgccatgactgccat--tttgtagcttgattgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
| | ||| || | || | || | | | ||| | | | ||| ||| | | ||| |||||| |||||||| ||||||||||| |||||||| || ||||| || || ||||||
--gaaaattaacaagcaatttatttcagctttggttgacattgttctcatatgtcttgagtttatttactatggtggaacttattccaattaacatttttagGTAAGGATGTCCTTGCCAAGGCCAAGACAGGCACCGGAAAAACAGTAGCCTTTTTG
upper sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 3
----ccggatcccctcaaatttgccatgactgccattttgtagcttgattgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
| | || |||| | | |||| ||| || || | | | | ||| || | ||| ||| | | ||||||| |||||| ||||| |||||||| || |||||||||||||| ||||| || |||||||||
ctattttaccgttgtttatgttcccatttattctatttagtatgtttctttaattctcagatttctgtgggg--ctta--ctctggtgagttgtgtttttatagGTAAGGATGTTCTAGCCAAAGCTAAAACAGGCACTGGGAAAACTGTCGCATTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
tcttaac putative branch site (score: 2)
tttcttccatgctctg putative PPT
tttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccggatcccctcaaatttgccatgactgccattttgtagcttgattgattgtttaaattcctcttaactccttggtttcttccatgctctgtttttccagGTAAAGATGTCCTAGCCAAGGCCAAAACAGGCACTGGTAAAACCGTTGCATTTTTG
- - - - cctcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctct