Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcttcttctcccaagagattcagacctatttgtggtggcttcttaatgattgttgaatgtgcatgttgcagGCAGACGTTGAGGTTGATGTGGCGGCGGCGGCGGCGGCGGCGGCTGCAGGGCAGCCAAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGGGTGGATC
Basic information
species | Glycine max |
transcript | GLYMA07G39980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g04790.t01 (Vitis vinifera), 3'ss of exon 1
gtgagttcttcttctcccaagagattcagacctatttgtggtggcttcttaatgattgttgaatgtgcatgttgcagGCAGACGTTGAGGTTGATGTGGCGGCGGCGGCGGCGGCGGCGGCTGCAGGGCAGCCAAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGGGTGGATC---------------------
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gtgagtccaaagccacagtgcatctgctgattaagcctttctctgtttctgacgttctttctctgccttctgtttagGCGGATGTCGAAGTTGATGTGGC---------------------CCCAGGAGTGCCGAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGTGTCGATTTGGATGCACTTCTCGACATGT
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S164_64V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagttcttcttctcccaagagattcagacctatttgtggtggcttcttaatgattgttgaatgtgcatgttgcagGCAGACGTTGAGGTTGATGTGGCGGCGGCGGCGGCGGCGGCGGCTGCAGGGCAGCCAAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGGGTGGATC---------------------------
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--------------------------------------------------------gcttgggtccgtgcgtatggatcgtgatctgagtttggtcttttacagGCGGATCCTGAAGTTGAAGTTGCACAGCCCAAGAAGAGAACTTTCAAGAAGTTCACCTTCCGAGGAGTGGATCTGGATGCCTTGCTTGATATGGGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcagacctatttgtggtggcttcttaatgattgttgaatgtgcatgttgcagGCAGACGTTGAGGTTGATGTGGCGGCGGCGGCGGCGGCGGCGGCTGCAGGGCAGCCAAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGGGTGGATC
tcttaat putative branch site (score: 3)
ttaatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcttcttctcccaagagattcagacctatttgtggtggcttcttaatgattgttgaatgtgcatgttgcagGCAGACGTTGAGGTTGATGTGGCGGCGGCGGCGGCGGCGGCGGCTGCAGGGCAGCCAAAGAAGAGAACGTTCAAGAAGTTCAGCTTCAGGGGGGTGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA