Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G161553_T01 (Zea mays), 3'ss of exon 2
--------gtaagtttttctttcccccttttgtttaacaagagccaa------aaatgctacaagtctattgaagatgtcgtggtgaatac-tggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
| ||| | ||||| ||| ||| || | |||| | | || ||| ||| | || | |||||| | ||||||||| ||||| |||||||||| || || || | ||||||||| |||| ||||||||||| |||||||| | |||
tcgaagttaaatgttaacagtctggagttttgctta-caatagttgtgtctttatgtgctttagtttaataccctttgtgtgtgtgtgtgtgtgtgtttagGTATATTGAAGAAAGACCATTTCGAAGATTTGTGGAGGCTTGCATAGAAGAAACAATCGTGGTCTATGTTGATCATCTCCTTTCCCAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
---gtaagtttttctttcccccttttgtttaacaagagccaaaaatgc-----tacaagtctattgaagatgtcgtggtg-aatactgg------atgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
|| | ||| ||| | ||| | || | | | | | || ||| | || || | || ||||||| || |||||| | ||||||||||||||| |||||||||| || || || | || |||||| | || |||||||||||||||||||| |||||
tctgtcaatttag-tttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA03G03120.2 (Glycine max), 3'ss of exon 21
--------gtaagtt-tttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagat------gtcgtggtgaatactggatgca-gGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
|| | || |||| | | || | | | || |||| | ||| | |||| || || | | | || || |||| | |||||| |||| ||||| |||||||| ||||| || ||||||||||||| ||||| |||||||| ||||| |||| |||
ttgctggtgtgaattgcttctattgcatttatttgaagtttgattgttaaatattt--agtttgttgaggaaaactaagtttcgaccatccatatattcaagGTACATTGAAGAACGATCTTTTAGGAGATTTGTTGAAGCCTGCCTGGAAGAAACAGTGGTTGTTTATGTTGATCATCTTTTAACACAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 20
------------------------gtaagtttttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
| |||||| | | | ||| || | || ||||| | | || | | || | || || ||||| | ||||||||||||||||| |||||||| ||||| || |||||||||| || ||||| |||||||| || ||||| || |||
aagtttgctgaatccagcctgttgatctacttttctgtgtctcattttcatattta-agttaaaaacatctcttatttactctaaatcttttgt---------gacaaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
------------------------gtaagtttttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
| |||||| | | | ||| || | || |||| | | | | | || | | |||| || ||||| | ||||||||||||||||| |||||||| ||||| || |||||||||| || ||||| |||||||| || ||||| || |||
aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatattta-agtttaaaacatctcttatttgctctaaatctt-ttgtgacta--------agGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
aaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA