Sequence
atgc intronic sequence ATGC exonic sequence...acattaacatcataaaagagttagaccaaatgtgataatatatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G56550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
--acattaacatcataa-aagagttagaccaaatgtgataatatatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
| | | | | || || | | | |||| | | | | || | ||| | | | || |||||| | | | |||||||||||||| | ||| | || ||||| ||||| | || ||||||||||| || || | ||| ||||||||||||||||||||||| ||| |
cttgtctgccgtggtgttgattattggaactg-tctcttaatttctttctcgtgtgtgg-tgctgagttttaaaatccattcttgtttatttcactgt-ctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
upper sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
acatta-acatcataaaagagttagaccaaatgtgataatatatgcaaagaatttgaatactgca--atccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
| || | || || | | | ||||| | | | ||| ||| || || | || | | || | ||| ||| ||| || |||| ||||||||| | || || || ||||| | ||||| | || ||||||||||| || || ||||||||||||||||||||||||||||| ||| |
-ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtt-tttgattgatttcattgtac-agGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
upper sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g04760.t01 (Vitis vinifera), 3'ss of exon 1
-acattaacatcataaaagagttagaccaaatg-tgataat-atatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
|| || | | || | || ||||| | || | ||| || | | | || |||| | | || ||| |||||| |||||||||| ||| | || ||||| ||||| | || || | ||||||||||||| || |||||||||||||| ||||||||||| ||||| ||| |
gctatacactgtctttctcattttcatttcttgctgatattgatcaatcatcaatgtggg-attagtttttgaagtttgat-tgcttgatttcattatac-agGGTTTCTTTAATTTTACTTCTCGAAGGCCTCGCCACCTACTGTACATTTTGGAGCTTGGATACAATGTTATGTATAATGATGTTGACATGGTATGGTTGG
upper sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S19_296V6.1 (Physcomitrella patens), 3'ss of exon 2
---------acattaacatcataaaagagttaga--ccaaatgtgataatatatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
|| || | ||| ||| | | | | | | ||| | ||| | | ||| | ||| | | ||| | || ||||||| ||||||||||| | || ||||| || | || | | ||||||||||||||||||| || |||||||||| || |||||||| |||||
acatgtttggcag-gacgttatattttggttgcattctgattccatttcttcctgccgcttgtctgag-atttcaaactaatg---agcgtggtttgatgtac------agGGTTTTTTCAATCTGACTGCGCGAAGGCCCAAATACCTACTGGAAATTTTGGAGCTAGGTTACAGCGTCCTGTACAATGACGTCGATATGGTGTGGCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
acctaat putative branch site (score: 3)
atgttttacctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattaacatcataaaagagttagaccaaatgtgataatatatgcaaagaatttgaatactgcaatccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - cataaaa
- - - - - - - - - - - -gaccaaa
- - - - - - - - - - - - - - - - - - - - - - caaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaatcc