Sequence
atgc intronic sequence ATGC exonic sequence...accatcgccatcactattaccatagtaccatcaccattaccatagtaccatcttcatcaccacatgatttggtgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05010.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G086497_T01 (Zea mays), 3'ss of exon 6
-------------------------------------accat-cgccatcactattaccatagtaccatcaccattaccatagtaccatcttcatcaccacatgatttggtgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA-
| | | || || | || |||| || || | || | | | | || ||||| | | | || || || || |||||||||| || | ||||| ||||||||||| |||||||| |||||||| |||||||| ||||| ||||| ||| | | | || ||| |||
gtaccttcttgcctatgacctgtcacttcgcttctgtgtagtgcttcttccttagttccttagtttgtgtactggtataactgtctgtggcttgtaatgaaattatttgtcgttgctgatttatttcgtatgttt-agGAGGAAGACATGCTCCTAGAGAACGTCTACTATTCTGAAATGAAGGATGCTGGGTTCTTCGATGCTGACTGGGATTAATCCGTGGC-TACTGTGCTGTATG
upper sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G30010.3 (Glycine max), 3'ss of exon 3
-------------------------accatcgccatcactattaccatagtaccatcaccattacca--tagtaccatcttcatcaccacatgatttggtgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
| | ||||| || | || | | | || ||| || | ||| | | | || | || | | ||||||||||| || ||||||||||||| ||||| || ||||||||||||||||| ||||| || || |||||| | | | | | | || | |
gtcataatggccttcacttaattcctggggttcagtttttattagtcaagccttggtattgtttgtagtttggacaatcctccttctttcattgatctgactaattgttgttatttgatgattatagGAGGAAGATTTGCATTTGGAGAATGTGTACTACTCTGAAATGAAAGATGCTGGTTTCTTTGAAGCAGATTGGAACTGATGTGGTATCGACTGCTAGATTA
upper sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G37380.1 (Glycine max), 3'ss of exon 5
----------------------------accatcgccatcactattaccatagtaccatcaccattaccatagtaccatcttcatcaccacat-gatttgg-tgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
| | |||| | | | || || ||| || ||||| | ||| ||| || | | | | | ||||| | | |||||||||||| || ||||||||||||| ||||| || |||||||||||||| || ||||| || || |||||| | | | | | | || | |
gtcataatgcccttcacttaatgcctggggttcagtttttactagtcaaaccatgttattgtttgtagt-taggacagtcttccttctttcattgatctgactagttgtagtta-ttgtgatgattacagGAGGAAGATTTGCATTTGGAGAATGTGTACTACTCTGAAATGAAAGATGCCGGTTTCTTTGAAGCAGATTGGAACTGATGTGGTATCGACTGCTAGATTA
upper sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------accatcgccatcactattaccatagtaccatcaccattaccatagtaccat-cttcatcaccacatgatttggtgctaaaattcacttgtgtttgctt------cagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
|| | || || | | || | | | || ||| | || || | | || | || | || || |||| |||||||||||| || ||||||||||||| ||||| || || ||||||||||| || ||||| || ||||||||||| | | | | | | |||
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccatcttcatcaccacatgatttggtgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
tgctaaa putative branch site (score: 2)
tttgcttc putative PPT
taaaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatcgccatcactattaccatagtaccatcaccattaccatagtaccatcttcatcaccacatgatttggtgctaaaattcacttgtgtttgcttcagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - -ccatcac
- - - - - - - - - - - - - accatca
- - - - - - - - - - - - - - - - - cattacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattca