Sequence
atgc intronic sequence ATGC exonic sequence...cagttgtagaagaattatgccttttttttttaatctaagacttagcattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
Basic information
species | Glycine max |
transcript | GLYMA12G03640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
-----cagttgtag-aagaattatgccttttttttttaatctaagactt--agcattttgaaaatgaaattcatatagtttgattactgtatttgatggcat----gaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
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gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
--cagttgtagaagaattatgcctttttttt-ttaatctaagacttagcattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
| ||| || | |||| | | | | ||| | | | | | | | |||||| | ||| || |||| || ||||||| | |||||||| ||||||||||||||||| || || ||||||||| | ||||| || || || ||||| |||||||| ||| |||| ||||| || |
ttcctttgccaaattttattgccataatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtat--ttatggtttttg-tgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA
upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 1
cagttgtagaagaattatgccttttttttttaatctaaga-----cttagcattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
| || | | | | ||| | || | || | ||| | | | | || ||| | |||| || ||| | ||| | | ||||| | |||||||||||||||||||| |||||||| || |||||||| | |||||||||||||| ||||| |||||||| | | | |||||||| |||
---tgataaagggctctttgttttctggttgggtgaaataaatttctttggctgtagctgataaaaggctcgccctttgttt--tgtttgtgacaataagtgcagTCTTTGCAAGCTCTGAAGAAGATATCCCAGGAGCAGCCTACTGCCTGTTTGCGAGCAGGTGCTCTAATGGCAGTGCTTTCTTTTCTTGACTTCTTCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
atttgat putative branch site (score: 5)
aaaatgaaattcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagttgtagaagaattatgccttttttttttaatctaagacttagcattttgaaaatgaaattcatatagtttgattactgtatttgatggcatgaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgaaa