Sequence
atgc intronic sequence ATGC exonic sequencegtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaatctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA
Basic information
species | Glycine max |
transcript | GLYMA18G16220.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G16220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 2
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaatctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA-----------
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---------aagttcagtc--tggtgatcagtgtat-gacatca---tttcagtcgtagttaattgcattagagctgt-actattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAAGTATTCAACAA
upper sequence: GLYMA18G16220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G160504_T01 (Zea mays), 3'ss of exon 2
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaatctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA
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---------aagttcagtc--tggtgatcagtgtat-gacatca---tttcagtcgtagttaattgcattagagctgt-actattctagtctaacgattttgctaaatggttgcagTCGTTGATGATTGCTGCAATCCCAAATATCATCGGTTGGCTTGCGATCTCCTTTGCAAAA
upper sequence: GLYMA18G16220.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01860.t01 (Vitis vinifera), 3'ss of exon 3
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaat-ctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA
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--------gtgctttagt-attgtgattgcgcatttgcatttgcattttctgattgcaggtgccataaaaatgaa------tttctgaatgttggt-tctttctgttgac-ttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA
ttttaat putative branch site (score: 3)
tttttttta CT-rich tract
tgttttttttaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaatctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC