Sequence
atgc intronic sequence ATGC exonic sequencegtaatataaagctagacaggtttaggttgtactgtaatcatagctttttaatctggtacaatgtctatgtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatattacagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G36440.1 (Glycine max), 3'ss of exon 11
gtaatataaagctagacaggtttaggttgtactgtaatcatagcttttt--aatctggtaca----atgtctatgtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatatt-acagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
||| | ||| | |||||| | ||| || || |||| |||||| | | | ||||| | | | | | ||||||| ||||| ||||||| | ||||||||||| || || || ||||||||||||||||||| || |||||||| || |||| ||| |||||||| ||||| |||
---------------------------tgtccattaacattttctttttcaagtcttgttcatgtcatgttcgataagtgctatgagtttt-tattcattaataat--ggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTAGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
upper sequence: AT5G58160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
gtaatataaagctagacaggtttaggttgtactgtaatcatagctttttaatctggtacaatgtctatgtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatatt-acagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
| || ||| || | | |||| | | | | | | | || || || || ||| | ||||| | | | | | | ||||||| ||||| ||||||| | ||||||||||| || || || ||||||||||||||||||| || |||||||| || |||| ||| |||||||| ||||| |||
-----------taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttat-----------tcattaata--ttggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
upper sequence: AT5G58160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0016g00160.t01 (Vitis vinifera), 3'ss of exon 6
gtaatataaagctagacaggtttaggttgtactgtaatcatagctttttaatctggtacaatgtctatgtgtcg---ctatgtctgccatgataattaaaagctaagtgtctctaaaatatta-cagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
| | | ||| || | || | ||| | || | | ||| | || | |||| | | | | | || || | ||||| ||||||||| | ||||| || ||| | |||| |||||||||||| ||||| || |||||||| ||||||| ||| ||||| ||| |||| |||
---------------------------tttgtagatgtcagcttttaattgtcagacacatccgtcaagtagcaagattttgtgaccaattgtccttaacaatcataaatttgtggaacatgaacagAATTCAGTGCTTGCTTTAGAGGATTCAGCTTTAGATGTTGATCAGGTTGATAACCTCATAAAGTTTTGTCCAACAAAAGACGAGATCGAGCTACTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatattacagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
ctctaaa putative branch site (score: 3)
ataattaaaagctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatataaagctagacaggtttaggttgtactgtaatcatagctttttaatctggtacaatgtctatgtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatattacagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA