Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgtcacttctaatatctatttctgattgtccatttcactggctttctgtaagttagtaactttatgttatggggctttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08350.2 (Glycine max), 3'ss of exon 2
---------------------gtgagttgtcacttcta-atatctatttctgattgtccatttcactggctt-tctgtaagttagtaactttatgttatggggct---ttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
|| || || | || |||| | | |||| | | | || | || | || || || | || || || ||||||| ||||| || || ||||| ||||| |||| |||||||| | ||||||||||||||||| ||||||||||||||||| ||||| || ||||||||
gtgagcatctctgtttaagtcttgttttatctgtcatatatatgcagtagtgatgccttactagaaatgcatatccagtattttgttgtttgaattttgaaacctaacttttagGTGCAATGGACACCAAATTATTGGAGGCACTGTATTGGAAAGGGATACCAGTTTTTGACATGGGCAGCCATATGAGCACAGTTGATGTTGGCTGGGGTTC
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G20730.1 (Glycine max), 3'ss of exon 3
----------------------------gtgagttgtcacttctaatatctatttctgattgtccatttcac-tggctttctgtaagttagtaactttatgttatggggct---ttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
| || | | || ||| | | |||| | | | || | || | || || || | || || || ||||||| |||||||| || ||| | ||||| | || |||||||| | ||||||||||||||||| ||||||||||||||||| ||||| || ||||| ||
gtgagcatctctgtttaagtcttgttttatctgtcatgtatattattatgcagtagtgatgccttactagaaatgcatatccagtattttgttgtttgaattttgaaacctacattttagGTGCAATGGATACCAAATTAGTGGAGGCACTCTATTGGAAAGGGATACCAGTTTTTGACATGGGCAGCCATATGAGCACAGTAGATGTTGGCTGGGGGTC
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 3
--------gtgagttgtcacttctaatatctatttctgattgtccatttcactggctttctgta-agttagtaactttatgttatgggg-----ctttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
| |||| || |||| | || || | | | || ||| || |||| |||| | ||| || | || ||||||| |||||||| |||||||| ||||| | || |||||||| | ||||||||||||||||| ||||||||||| |||| ||||| || ||||| ||
tcatgtgtttttgttgagttttgtaattgcccttgctagagatgcgtatc--tggtattgtgtacagttgactaaagagggttctgaaaatctaccttttagGTGCAATGGATACCAAGTTATTGGAGGCGCTTTATTGGAAAGGGATACCAGTTTTTGACATGGGCAGCCATATGAGTACAGATGATGTTGGCTGGGGGTC
upper sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G09650.1 (Glycine max), 3'ss of exon 1
--------------------------------------------gtgagttgtcacttctaatatctatttctgattgtccat-ttcactggctttctgtaagttagtaact-ttatgttatggggctttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
| |||| || |||| | ||| | | | | | | | | | || || || || || | | || ||||||| ||||||| |||||||| ||||| | || |||||||| | || |||||||||||||| ||||||||||| |||| ||||| || ||||||||
gtgagtctcacgatttaagccttctatttttctctatcatgtgcttttgttgagttttgtaattgccattgttagagatgcgtatctggtagtgtacagttgactaaaaagggttctgaaaatctaccttttagGTGCAATGGATATCAAGTTATTGGAGGCGCTTTATTGGAAAGGGATACCGGTTTTTGACATGGGCAGCCATATGAGTACAGATGATGTTGGCTGGGGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccatttcactggctttctgtaagttagtaactttatgttatggggctttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
tagtaac putative branch site (score: 1)
taactttatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgtcacttctaatatctatttctgattgtccatttcactggctttctgtaagttagtaactttatgttatggggctttatagGTGCGATGGATACAAAGTTATTAGAGGCTTTGTACTGGAAAGGCGTTCCAGTTTTTGACATGGGAAGCCATATGAGCACAGTGGATGTCGGGTGGGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA