Sequence
atgc intronic sequence ATGC exonic sequencegtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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---------gcaagttaacctg-gttgctgggtatcagttctataatgcctcat-----tgggctgtttgttcataaaatta-attttattgatgctgatgcagGTACGAGAAGAGGCACTCCAATATTCCTGCTCACATTTCACCGTGCTTCCGTGTTAAGGAAGGAGATCACGTGATCATTGGCCAGTGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 4
gtaccagaggcaagctaatcttcaata---ttggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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-----------gtattccccttccatacctttggtgagcagttattgttgtttacatggacagaagtaactaatgtttc------ttctttgctcat-tctatttagATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G11430.1 (Glycine max), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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gtattattctcctgcaatccttttgtgttcattttgttttgtt--tcgttttgtatgtttggagaaacataattataatt--ccattttcatttttatgctcagGTACGAGAAAAGGCACTCCAACATTCCTGCTCATATATCACCTGCTTTCCGTGTGAAGGAAGGAGATCACGTTATTATTGGTCAATGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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--------------gtaaattcatacatt--ctcatacttctt--tccatagagtcttacacattgatgtttaagaaagtaatatcctttttgttctt----agGTATGAGAAGAGGCATTCAAACATTCCGGCTCATGTCTCACCATGCTTCCGTGTTAAGGAAGGAGACCATATCATCATTGGCCAATGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtg--tagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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---------gtaagtacattgtga---tgaacctatgttc-ttgatagagctgcgcaaagatataacatcaatgctgataaacgattatcttaaatttttcattagATATGAGAAGAGACATTCCAACATCCCTGCCCATGTCTCACCGTGTTTCCGTGTCAAGGAAGGTGACCATGTCATCATTGGCCAATGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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--gtaggaaccgatttaatt----gaatgaatctttgtttttcgg--gctcctttctcttgtatggaatat------aatattaaattgt-attgtcactctagATATGAGAAGAGGCACTCAAATATACCAGCACATATATCCCCATGCTTCCGTGTCAAAGAGGGTGATCATGTTATTATTGGCCAGTGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttg-----tgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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---------gcatgtt--cctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ16024 (Selaginella moellendorffii), 3'ss of exon 4
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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-------gtgagtgttaggcccaagttcttccaagtttcttctttcgtcctcgcgattctctcgcgattctcatccaa---aaaattcttt--tttttattcagGTATGAAAAGAGGCACTCAAACGTGGCAGCTCATGTGTCGCCGTGCTTTCGTGTCAAGGAAGGAGATAAAGTGATCCTCGGCCAGTGCAG
upper sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ07974 (Selaginella moellendorffii), 3'ss of exon 4
gtaccagaggcaagc-taatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
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---------gtgagtgttggcccaagttcttccaagtttcttctt-tcgcctcgcgattctctcgcgattctcatccag--aaaaatctctt----ttttttcagGTATGAAAAGAGGCACTCAAACGTGGCAGCTCATGTGTCGCCGTGCTTTCGTGTCAAGGAAGGAGACAAAGTGATCCTCGGCCAGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
aactgat putative branch site (score: 3)
ataatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttgtgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA