Sequence
atgc intronic sequence ATGC exonic sequence...aagatagagaacactgcagtatatgataactgttgttggattgcaaactatctccatactctgctattaatgccaatctttgggtttctgcaactggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
Basic information
species | Glycine max |
transcript | GLYMA06G02110.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
aagatagagaacactgcagtatatgataactgttgttggattgcaaactatctccatactctgctattaatgccaatctttgggtttctgca-actggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
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agcattgcagtaatgccatggttctacatttatt-tggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 4
aagatagagaacactgcagtat-atgataactgttgttggattgcaaactatctccatact-ctgctattaatgccaatctttgggtttctgcaactgg-cagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
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--tatgtgatccattatgacaccatgttccatgtaactccgtggtag-ttatgtgtattctgttgttccatatgcataactatgaccatcttctgcttttcagATAATTGATGCTGTTGTTGCTGCACGTATCTTAAATGCCACACTTGTTGTTCCCAAATTGGATCAAACATCTTTCTGGAAAGATGCAAG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T02 (Zea mays), 3'ss of exon 4
aagatagagaacactgcagtatatgataactgttgttggattgc--aaactatctccatactctgctattaatgccaatctttgggtttctgcaactggc-agATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
|| | | ||| ||| ||| | | || ||| | | | || | || | | | ||| | |||| || | |||| |||||||| |||||||| || || ||||||||||| ||||| ||||| ||| |||||||| ||||||||||||||| || ||
cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgcttt-ctctatagacgaattat--aacccctgctgctctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T03 (Zea mays), 3'ss of exon 4
aagatagagaacactgcagtatatgataactgttgttggattgc--aaactatctccatactctgctattaatgccaatctttgggtttctgcaactggc-agATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG-----------
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cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgcttt-ctctatagacgaattat--aacccctgctgctctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAGGTATGCGATAG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G131699_T01 (Zea mays), 3'ss of exon 4
aagatagagaacactgcagtatatgataactgttgttggattgcaaac-tatctccatactctgctattaatgccaatctttgggtttctgcaactggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
|| | ||| || | ||| | | | | | || | | | | || | ||| || | | || ||||| | ||||||||||||||||| || ||||| ||||| || ||||| ||||| ||| | || ||| ||| ||||||||||| || ||
-agtccacatgagtttttttatgctttagtgataattgtaatacttatatgccttgttgttatctttatagacctaattaacatgtgtattgctctttcagATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 4
aagatagagaacactgcagtatatgataactgttgttggattgcaaactatctccatac-tctgctattaatgccaatctttgggtttctgcaactggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
| || | | | || || | | ||| | ||| | || | || | || | | | || | ||| |||| | | ||||| || ||||||||||| ||||| || ||||| |||||||||||||| ||||||||| ||||||| || || |||| || ||||
actatggtgc-tattgttgttttaccttttagttacagaattttttatcatattattaaatttgttgctcaggctgagcttgttacacctgccattttcagATAACTGATGCTGTTGTCGCTGCCCGCATTTTAAATGCTACTCTTGTCGTTCCAAAACTGGATCAGAAGTCCTTTTGGAGGGATGCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactatctccatactctgctattaatgccaatctttgggtttctgcaactggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
tattaat putative branch site (score: 2)
tttctgc putative PPT
tattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagatagagaacactgcagtatatgataactgttgttggattgcaaactatctccatactctgctattaatgccaatctttgggtttctgcaactggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
- - - - - -cactgca
- - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - gattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg