Sequence
atgc intronic sequence ATGC exonic sequence...ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48640.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
| | | | || || || || || | || | || || || | | || ||| || | || | | | || | || |||||||| ||||| || || ||||| || |||||||| || || || |||||| | ||||| |||||||||||||| |||||||| ||||| || || ||
gtcagtcc-tac-tatcttcttcatcttcatctgaacgaaga-acacacgaacgaaccaagaa-att---aatctaactgaattcttgaatttttgc-agGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G149216_T01 (Zea mays), 3'ss of exon 2
ttgaat-acatatgtagttttttaatttcttactacataaatttacttttgatttgattagta-atattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
||| | | | | |||| | || | ||||| | || | | | | | ||| | ||| | | ||| | | ||||| || ||||| || || |||| || || |||||||| || || |||||| ||||||| |||||||||||||| |||||||| || || || || ||
-tgattcaattgtacgagcgattaactcgttgtcagataaagattattagggggtcacgggcagataaatggttcattgttgattattggcgtgcacac-agGGGCCCTGGCATCGCGGTGATGATCCTGTCGTGGATAATCACCCTATACACGCTATGGCAGATGGTGGAGATGCACGAGATGGTGCCTGGGAAGCGGTTC
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattag--taatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
||| | | | ||| | || |||| | | | | || | | || || | | ||||||| ||||| || ||||| || || ||| | | || ||| | || || || |||||| | ||||| |||||||||||||| |||||||| |||||||| || ||
----gtacgcacacggcacatc---ttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgttgtcaaat---ggcatatatgc-agGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
----ttgaatacatatgtagttttttaatttcttac-tacataaatttacttttgatttgattagtaat--attcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
| ||| ||| | || | | || | ||| |||| | | | | | | ||| | || ||||||| ||| | ||||| | |||| ||||| || | | || || || |||||||| || || || ||||| ||||||||||||| ||||||||||| |||||||| |||||||| |||
atggtataatgt-catgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgaga-attacaatgtcctcttataca-----gGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G24520.1 (Glycine max), 3'ss of exon 1
ttgaatacatatgtagttttttaatttct-tactacataaatttacttttgatttgatta-gtaatattcgtgat---attacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
|| ||| | || || | | | ||||| ||| | | || | | ||| ||| ||| | ||| | | || | | | ||||| || || || | || || | || |||||||| || || | ||||| ||||||||||||| ||||||||||| |||||||| |||||||| |||
-----tagataaacaacattatagtatatatactatgcgtttttgttatggaaagaaaaatgtactatgcgttttttaatttgagaatcactatgctttcttcagGGGTCCCGGTGTAACTGTGCTAGTCCTGTCATGGATCATTACCTTGTACACCCTATGGCAAATGGTAGAGATGCATGAAATGGTTCCTGGAAAACGTTTT
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
-----------ttgaatacatatgta--gttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
| || | ||| | | | || || ||| || ||| | | | || || ||| ||| | || || || | || || || | ||||| || || || | || || || || |||||||| || || || ||||| ||||||||||||| ||||||||||| ||||| || |||||||| |||
cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatactatactatgcgtttttta-----atttgaga-atcactatgttttttt-------tcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
ttgaata-catatgtagttttttaatttcttactacataa--atttacttttgatttgattag--taatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
| || | | ||| ||| || | | | | | ||||| | ||||| ||| | ||| || ||| | ||| | ||| | | | | ||||| || || | | | || | ||||||||||| || || |||||||| ||||||||||||| |||||||| ||||||||||| || ||| | |||
--gtatgtcttttgtgtctttacaagagatagttgccttattatttatgtctgattccatttgattaaggttgaacataa-aaaaaatattgatcttt---tcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT
upper sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
| || || || | ||| ||| | || || | || | | | | | ||||| || || || || || | || || |||| | || || |||||| |||||||||||||||||||||| |||||||| || || |||||
----------------------------------------gtaacgttcgaat--gtta-taacgtctac-attttttagggttct-tcgttt-ttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
atttgattagtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattagtaatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- gaataca
- - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - -gatttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaagt