Sequence
atgc intronic sequence ATGC exonic sequence...atacacctcagaaaaagaactagagggactacatcgtaaactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g09430.1 (Oryza sativa), 3'ss of exon 2
-atacacctcagaaaaagaactagagggactacatcgtaaactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
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gaaagttgtcatgaccataaattt-gtgacgatgctatggtttgaacatctatttgcactcctacaaaatttgtcttttgttgcttttgccatggcaacagGACAATCCTTGGATTTTGGGCTGGCCATCGCAATTCTAAAATAAGAGTCATTTTGGCACAAGTCTGGGAGAATGATACAGAGCTTGCTATCAGTAACAAT
upper sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G33330.1 (Glycine max), 3'ss of exon 3
atacacctcagaaaaagaactagagggactacatcgtaaactctatttgctcttagccta-ttactaattat-attttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
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actgatgatggtgcaatga-tacgtagtttgttctgtaagatcaatagacaatggttctacttattgattctgaaaatttgataattttatgcttttgc-agGACTACTCTTGGATTCTGGGCTGGTCATCGGAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT
upper sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G02630.1 (Glycine max), 3'ss of exon 3
------atacacctcagaaaaagaactagagggactacat-cgtaaactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
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atgatgcaataatatgtagtttgatctgtaagatcaacagacaaggattctacttgcat---atttattgattctgaaaatttg--ataaatttgtgctttg--cagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT
upper sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0218g00090.t01 (Vitis vinifera), 3'ss of exon 3
----atacacctcagaaaaagaactagagggactacatcgtaaactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
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tagcatgtttctcatacaacgaattgaatgtaa-gttttatgtggatggaaagatcccagt-tatga--gattattgcctaaaattgagaagcatactttgcagGACAACTCTTGGCTTTTGGGCTGGTCATCGGAACTCCAAAATTAGAGTTATACTAGCACGTGTATGGGAGAATGACACTGAACTTGACATTATGAACAAC
upper sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
atacacctcagaaaaagaactagagggactacatcgta--aactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
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--gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
tactaat putative branch site (score: 1)
tattactaattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atacacctcagaaaaagaactagagggactacatcgtaaactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - -agaaaaa
- - - - - - - - - - - - - - ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg