Sequence
atgc intronic sequence ATGC exonic sequence...ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
Basic information
species | Glycine max |
transcript | GLYMA15G00590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
--ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
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tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctcca-tggttgcttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
upper sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 5
-----ctagtttttaaaaca-aaccataac--tttccatttcttttttctgcattctctt-taacttct-atttat---cttaatcttgaa------attttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
|||||| | | | | | | || | | |||||| || |||||| | | | || ||| |||| ||| || || | || |||||||||| ||||| ||||| || |||||||| ||||| || || |||||||||||||||||||| |||||||| || |||||||| || ||||| | ||
gcatgaggttttttatgttacagtggtgatgatgttgatgggaaatattctcattctgttataacttatcaaccaaatgctgaataatgaatcaatcattggtttttctttgaatacagTAATTGGAACAGCATTTGCTTTAAACATGCTATTCAATATCCCGGTTTGGATTGGTGTTCTTCTCACAGGACTTAGTACATTGATTCTTCTAGCACTTCA
upper sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 5
ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttat-tgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
|| | | | || | ||| | | | ||||| | | ||| || | |||| | | || ||| | || | || ||| || || ||||| ||||| ||||||||||||| | |||||| || ||||| ||||||||||||||||| | || || |||| || | ||| | ||
gtatcacacttgtttactctttacagtgtgattcaatactaacctctctctgttgatactaattgccaaaatcg-gttttcttatatatatatatatatagTTATCGGAACAGCTTTTGCTCTGAACATGCTCTTTAGCATACCGGTGTGGATCGGTGTTCTTCTGACAGGCTTAAGTACGCTGATTCTTCTCGCACTTCA
upper sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 6
--ctagtttttaaaacaaaccataactttccatttcttttttctgcat-tctctttaacttctatttatcttaatcttgaaattttttat-tgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
| |||| | || | | | || | |||| | || || || | || | || | | || | | || ||| | || | || | | | |||| ||||| ||||||||||||||||||||||||||||| || ||||| ||| |||||||||||| ||||| || || |||||| | || |||| |||||
taatggtttcttaagtgcatcct--ctcttcattattattaacttgatgtgtcatgcacatttcttcaacctattct--gatttctgcatgtttctttttccagTGATTGGAACAGCCTTTGCATTGAACATGCTCTTCAATATTCCTGTGTGGTGTGGTGTTCTTCTTACAGGGCTTAGTACATTGGTTCTTCTAGCTTTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
tcttaat putative branch site (score: 3)
tttaacttctatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
- - - - - - acaaacc
- - - - - - - - - - - - - -ccatttc
- - - - - - - - - - - - - - - - - - - ttctgca