Sequence
atgc intronic sequence ATGC exonic sequencegtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 6
gtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
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------gttacaatgccatttttcttttggtttgatatggtttagc-ttactcatattttgtcttatgcaatatgcagtttgtatgt---tttagcagctaagccttgacaata---aaatatattatatgaagaccatatagtgttgagctttcctcacatt-----agttttgagagcagctgacctgtgttttagGTGGTGTTGTTGCATCTGCTGCATATAAAAAATGGGAGAGAGCTGCCATGGCTGGTGTTTCTTTGGTTGCTGATGCAGCTGAAGAGCTTGAGCGCAACAC
upper sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 6
gtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
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gtga-cac-tgctttttttttttttggtttcatgtggcacacc--ctttacttttttcattttatgcgatatgcagtctgtatgtcttagctaaat-gtcgataatccaataaatt---ttattatgt----gagct-taaagtgtcgaattttccttacaat-----agttttgagagcagtggacttgtattttagGTGGTGGCATTGCATCTACTGCATATAAAAAATGGGAGAGAGATGCCATGGCTGGTGTTTCTTTAGTCGCTGATGCAGCTGAAGAGCTTGAGCGCAACAC
upper sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
gtgggcgcatgttctctgttagtctgttcttttgtta--tgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactat---caaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtg-gatagatggtgacctgt--gttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATG--GGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
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---------------------gtttttcctcatgataatcggataatatatatttaaaatttaaagta-aatttgcattagccaaagttt--ttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctg--cttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGA-GCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGA--AGTTTTATCCT-----
upper sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
gtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaa-actatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC---
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-----------------------gtgatctttttcaattccct---tcaagatctcatttacca-----gttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttc-ttactttacagtaataactaggttctctttatttctca-gGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
cattaat putative branch site (score: 3)
attaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT