Sequence
atgc intronic sequence ATGC exonic sequencegttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatctttatttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G41180.1 (Glycine max), 3'ss of exon 6
--------------gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatctttatttgagtgtaatgatgaaatgtgca-catatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG--
|| | ||| || | ||||| | || |||| | || || || ||| | ||| |||| | | | | ||| ||| ||||||||||| | ||||| || ||| | |||||||||||||| | | |||||| ||| ||||||||||||||||||
gttttgaaactttctttgtttgtgtacctt-ttactctaatttccaatctgataataaattcttg---ttaattgaattgtggtgattgttttcttatcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAGTG
upper sequence: AT3G20840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g01800.t01 (Vitis vinifera), 3'ss of exon 2
------gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatcttta-tttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
||| ||||| || || | | | | | | |||||| |||| |||| | ||||| || | | ||| || ||| ||| ||||||| || | ||||| ||||| || |||||||||||||||||||||||||| || || || ||||| | ||||
gtggatgtt-gatatttg---tatagatttctaattcaaaattttaat--tttttcaatctggaatttgaa---aagggtatgtggtgggaatgtagGCATAGATGGACAGGAAGGTATGAAGCTCACCTTTGGGATAATAGTTGTAGAAGGGAAGGACAATCAAGAAAAGGTCGCCAAG
upper sequence: AT3G20840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
----------gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatcttt--atttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
| || || | | || | | | ||| | | || | || ||| || | | | || ||| | | ||| ||||| |||||||| || || ||||||||||| ||||| |||| |||||||| |||||| || || | ||||| ||||||
ggcgcagagagctaaattttagcctggcgaaggtcgaagttg--ttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaatgattttgtgatctttatttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
ctttaat putative branch site (score: 4)
atctttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatctttatttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA