Sequence
atgc intronic sequence ATGC exonic sequencegcaatgatgaagcttattctgtggaccccttcagcaccattgcactttattcatcttctagattatagatgattgcccataagagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCATAAGCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G163104_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 3
gcaatgatgaagcttattctgtggaccccttcagcaccattgcactttattcatcttctagattatagatgattgcccataagagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCAT-AAGCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
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-----------------------------------gttagtatgaatgttgtgctaccaatcctatcagcagttatttatttctgtcca-tgtc--taatctgagtggtggttattctatttaagATGTTAAGAACAAGTGGGAGAATAGCTCATGGGGCAAGAAGCTAATTGTCCAGAAGAGGAGAGCGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTT-
upper sequence: GRMZM2G163104_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G27090.1 (Arabidopsis thaliana), 3'ss of exon 3
gcaatgatgaagcttattctgtggaccccttcagcaccattgcactttattcatcttctagattatagatgattgcccataagagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCAT-AAGCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
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------------------------------------------------gtgagtgctgcgtaatgtaaatatttgaattttgaagtgt-------ttcaatc--ttaactggaaaagtcttgcagATGTGAAGAACAAGTGGGAGAAAAGCTCATGGGGTAGGAAGCTTATCGTGCAGAAACGTAGGGCTAACCTTAACGACTTTGATAGGTTCAAGATCATGTT-
upper sequence: GRMZM2G163104_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 4
gcaatgatgaagcttattctgtggaccccttcagcaccattgcactttattcatcttctagattatagatgattgcccataa--gagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCATAA-GCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
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-----------------------------------------gtaaaggacatatgggaaaaatggtaactc-ttatccatgtttgataatcctttttctcgtttatcctaaattcttttgatggcagATGTTAAGAACAAGTGGGAGAATAGCTCCTGGGGCAGAAAGCTGATTGTGCAGAAGAGGAGAGCATCTCTTAATGACTTTGATAGGTTCAAGATCATGTT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgcccataagagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCATAAGCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
agttaat putative branch site (score: 4)
cttgttattctttttc putative PPT
ttgttattcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaatgatgaagcttattctgtggaccccttcagcaccattgcactttattcatcttctagattatagatgattgcccataagagaatagtgacacttagttaatcacttgttattctttttcagATGTGAAGACCAAGTGGGAGAACGGCTCATGGGGCATAAGCTGATTTTCTAGAAGAGGAGAGCAGCGCTCAATAACTTTGATAGGTTCAAAGTCATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG