Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatctatcatacatgttttgttataagtccaccattaaatgaaagtgcatctctattgaagtctttaataaaaacatatgtatgctatgcacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52700.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G22420.1 (Glycine max), 3'ss of exon 3
-------------------gtaagaatctatcatacatgttttgttataagtccaccattaaatgaaagtgcatctctattgaagtctttaataaa-aacatatgt----atgctatgc---acagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
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gtaagaaataaactttcctattctgcttttgtacaaacatattctcactttatccctataatattctgataaatctattctcgtgtacaaaatatatgatgtttgttatgatgtgatgtggtgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTAACCATACTTGGTGGTTTTTCTTGCACTGCAT
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G03670.2 (Glycine max), 3'ss of exon 3
----gtaagaatctatcatacatgttttgttataagtccaccattaaatgaaagtgcatctctattgaagtctttaataaaaacatatgtatgctatg-cacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
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ttttgtacaaacatattctcactttatccctataa-tattctgataaatcta--ttctcttgtac-aaaatatatgatgtttgttatgatgtgatgtggtgcagATAAAATGGATTTGCCCAACTGCTCCTTCTCGCCCTGTAACCATACTTGGTGGTTTTTCTTGCACTGCAT
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 4
------------------------gtaagaatctatcatacatgttt-----------tgttataagtccaccatta-aatgaaagtgcatctctat----tgaagtctttaataaaaacatatgtatgctatgcacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
|| || || | || || || | || | | |||| | || || | || ||||| ||| || | | | || | ||||| || ||||| ||||||||||||||| ||||| |||||| | |||||||| | | |||||||| ||| | |||||||| |
gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatg-atatgatgca--gATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
upper sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g06010.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaatctatcatacatgttttgttataagtccaccattaaatgaaagtgcatct---ctattgaagtctttaataaaaacatatgtatgctatg-cacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
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---------------------------gtaaggat-ttgtttttttaaattgcttttgggcttataaaaccacaaatcttactgttcaaattctatgatgcagATAAAATGGATTTGTCCAACTGCTCCTACTCGTCCTGTTGCAGTACTCGGTGGATTTCCTTGCACTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaagtgcatctctattgaagtctttaataaaaacatatgtatgctatgcacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
ctttaat putative branch site (score: 4)
tctttaataaaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatctatcatacatgttttgttataagtccaccattaaatgaaagtgcatctctattgaagtctttaataaaaacatatgtatgctatgcacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA