Sequence
atgc intronic sequence ATGC exonic sequencegttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacac-ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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-------------------------------------------gttacatggtcacatacctttttactcactagagctgt--ttttatttaacatgtttacaaatcttagttgt-taggtcagatctcct--tgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacac-ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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gtaacatggtcacatctattactgtttttgtttttcactagttct---------------gtttttatt---taacatgtttacaaaatat--tagttgttacttgttaggta--------cagacttcct--tgatgattcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaa-tataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA-
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---------------------------------------------------------------------------aatattaatcaagctatcatattctt-tatcagagtttgatgttaat--agctaccatt---caatggatttttgtggctgatt--cttatgtaatacttgtt-gcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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-----------------------------------------------gatcttttcgtaggttatgattataaatca-----agctaatata---ttcctttttt-ttgcttaccatatattag--taactgtt----------tcttataatat-------------atacttgat-gcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactc-attcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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----------------------------------------------------------------------------aattttaatcaagctatcattttc--tttatcagattttgatggttaa--tatctaccatttaatggatttgtgttgctgatt--cttatgtaatacttgtt-gcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
gttacaaagcttc--ctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatc-attttttggctaataa-aacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttc--tcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatag-tgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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-------------------------------------------------------------------------------------------------------gttttgtgtggctgtatattc--ttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttat--gcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
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-------------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgca---tgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
ggctaat putative branch site (score: 3)
cacttttcc putative PPT
attcttatcatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA