Sequence
atgc intronic sequence ATGC exonic sequencegttacgtgtttgattgtcaaattgaacagtaattttcactgaatggatatcccttctaaagtttaaaagtttgtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
Basic information
species | Glycine max |
transcript | GLYMA09G39270.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 5
-----------------------gttacgtgtttgattg--tcaaattgaacagtaattttcactgaatgg-atatcccttctaaagtttaaaagttt--gtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
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gttaagtgttaacttctttgcctttgatttatttgagaggttaaaatgctgcagcctctgttgtttgatgatgcatttttatgacaatatatattttttgaagtagATTTCATACATTTCCCAGAACTGGCCAGTTCTACATGTGGTGGCAAGCAATGATGGGATGTACTTGGCAGTTGCTGGCTCTCACGGACTAGTGCTATATG
upper sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G052750_T01 (Zea mays), 3'ss of exon 5
-------------------gttacgtgtttgattgtcaaattgaa---cagtaattttcactgaatggatatcccttctaaagtt--taaaagtttgt----gtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
|| ||| ||| | || || | | || | || || || | || | | | | || | ||| | |||| |||| || |||||||| |||||||| ||| |||||||| || ||| | ||||| |||||||| ||||||||||| |||||| | | | ||||
gttaagtgttaactcccttgtctttgatttatttgagaggttaaaatgctgcaacctctgttgtttgatgatgcatttttatgataatatatatttttcgaagtagATTTCATACATTTCCCAGAACTGGCCACTTCTACATGTGGTGGCAAGCAATGATGGGATGTACTTGGCAGTTGCTGGCTCTCACGGGCTAGTGCTATATG
upper sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 6
-------gtta-cgtgtttgat-tgtcaaattgaacagtaat--tttcact---gaatggatatcccttctaaagtttaaaagtttgtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
| | | | | | | | | ||| || | || | ||||| ||| || || | || | ||| || || |||||||||||||| |||||| |||||||||||||| |||||||||||| ||||||| | ||||| || ||||||||| | || || |||| |||||||
gttgagtatcatcatatccgttatccccttttgctcattcatcgtatcactttgaaataaatttcttatatatattttc----ttggtccagGTTTCTTATATTAGCCAAAATTGGCCTGTTCAACACGTGGCAGCTAGCGAGGATGGGAAATACTTGGCGGTTGCTGGTTTACATGGCCTGATTTTGTATG
upper sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 6
-------gtta-cgtgtttgat-tgtcaaattgaacagtaat--tttcactgaatggatatcccttctaaagtttaaaagtttgtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
| | | | | | | | | ||| || | || | ||||| ||| | || | | || || |||||||||||||| |||||| |||||||||||||| |||||||||||| ||||||| | ||||| || |||||||| | || || |||| |||||||
gttgagtatcatcatatccgttatccccttttgctcattcatcgtatcacttttgaaataaatttcttatatatgttttcttggtccagGTTTCTTATATTAGCCAAAATTGGCCTGTTCAACACGTGGCAGCTAGCGAGGATGGGAAATACTTGGCGTTTGCTGGTTTACATGGCCTGATTTTGTATG
upper sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 6
gttacgtgtttga-ttgtcaaattgaaca---gtaattttca----ctgaatggatatcccttctaaagtttaaaagtttgtg-tagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
||||||||||| | || | | |||| | || |||| | || | || || |||| | |||| | |||||||||||||| |||||||| ||||||||||||||||||| |||||| ||||||| ||||||||||||||||||||||| || || || || || || |
gttacgtgtttaaattatgtacttgataattcgttgtttttagtctctattttattaatgctcctaatatagttctctttgggctagGTTTCTTATATCTCCCAAAATTGGCCTGTTCAACATGTGGTGGCTAGCAAGGATGGGATGTACTTAGCAGTTGCTGGTCTCCATGGCTTAATCTTATACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacagtaattttcactgaatggatatcccttctaaagtttaaaagtttgtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
ttctaaa putative branch site (score: 2)
taaagtttaaaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacgtgtttgattgtcaaattgaacagtaattttcactgaatggatatcccttctaaagtttaaaagtttgtgtagGTTTCTTATATTTCCCAAAACTGGCCTGTTCAACATGTGGCAGCTAGCCAGGATGGAATGTACTTAGCAGTTGCTGGTCTTCACGGTTTGATATTGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA