Sequence
atgc intronic sequence ATGC exonic sequencegtatgtagcttttcttttctgtcagtgttcttattcatgttgatccatttcacaaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52150.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G01940.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------gtatgtagcttttcttttctgtcagtgtt---cttattcatgttgatccatttca-caaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
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gtaaatgactctaaaaattcttatccaaaaatttgtatttgattagatattgtagttaataacaatggtctagtcccactgttaagttcttctatgcacatgtgtctaaatcattcttaatgtgtgccttagATCTGCGAGAGGTCTCTTAAAAATACTCAAAATGGTCCAAGCATGCCTCCCGTGCAGCATTTTGTTAGAGCTGAGATGCTGCCTAGTGGGTACCTGATCA
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G21620.2 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------gtatg-tagcttttcttttctgtcagtgttcttattca-tgttgatccatttca-caaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
|| | | | || |||| | ||||| |||| || || | | | | ||| | ||| | || ||||| || ||||| | |||||||||||||| || ||||| | || ||| ||||||| |||||||||||||| | ||||||||| ||||
gtaaatgactctaaaaattcttatccaaaaatttgtatttgattagatattgtagttaataacagacctcacccgtgcaatggtctactcttactgttaa-gttctccttcaatgcatatatgtctaaatcattcttactgtgtgccttagATCTGTGAGAGGTCACTTAAAAATACTCAAAATGGTCCAAGCATGCCTCCTGTGCAGCATTTTGTTAGAGCAGAGATGCTGCCTAGTGGGTACCTGATCA
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------gtatgtagcttttcttttctgtcagt--gttcttattc-atgttgatccatttca-caaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
||| | | | | | | ||||| ||| ||| || | | | | |||| | || | || ||||| || ||||| | |||||||||||||| || ||||| | || ||| ||||||| |||||||||||||| | ||||||||| ||||
gtaaatgactctaaaaattcttatccaaatttttttatttgattaaatattgtagttagcaacagacctcacccatgcaatggtctactcccactattaagttctccttctatgcatatatgtctaaatcattcttaatgtgtgcctcagATCTGTGAGAGGTCACTTAAAAATACTCAAAATGGTCCAAGCATGCCTCCTGTGCAGCATTTTGTTAGAGCAGAGATGCTGCCTAGTGGGTACCTGATCA
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------gtatgtagcttttcttttctgtcagtgttc------ttattcatgttgatccatttcacaaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
|||| || | | ||| | | | | || |||| |||| | | | | | |||| || || ||||| ||||| | ||||| |||||||| || ||||||| || ||| |||||||||||||||| ||||| | ||||| |||||||||
gtatgtgttcataaagtcgtcttgactgaattgtcctcttagccttgttctattgttttcctcccatcaatcaactatcttgaagtcattcaaattttctgatgtaatgctcagGTCTGTGAAAGATCACTTAAAAATACTCAGAATGGTCCAAGCATGCCACCAGTGCAGCATTTTGTGAGAGCAGAAATGCTGCCAAGTGGCTACTTGATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcagtgttcttattcatgttgatccatttcacaaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
tgttgat putative branch site (score: 4)
tttaagaaatcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtagcttttcttttctgtcagtgttcttattcatgttgatccatttcacaaggtttaagaaatcttatagGTGTGCGAGAGATCTCTTAAGAGCACTCAAAATGGTCCTAGTATGCCACTGGTTCAGAATTTTGTGAGAGCAGAGATGCTTTCCAGTGGGTACTTGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG