Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattca-catat--agcattattat--acagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gtatgttgaaacaaatgaattacc-atgctttgttcagaataatcct--cttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
gtatgttgcaact-tttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gtttgtttcaaatgtttcatgaacacattatttttttc-------tctgtctgacacattgttgctgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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---------------gtttgtctcaatttct--catgcaataattatccctccctgacttat-tgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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------------gtttgtctcaa-----cttctcaagtaataattatccctccctgacttat-tgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gtttgtttca----tgaatacataattttttttcttggtctgac----------acattgttactgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtac-cctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactc----------ttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gtcggtttta--tttgcatatacataccttttccttg--tcagcaattctttctatat----gctaaattcatttctac--ttgtgat--agGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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----gttg-gtcattaatttccttaatgtctttgtttgt---tgtatttattcatcttttc------attggcatgtatctttgatgaatagGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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gtctgttataa-ttctcttacaagcacacttttt---------gtgtggcttagccgatt----gttactgacatggaactttttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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---------------------gttggttgtcttcgtttgacaagt-tacatacatgacttttgtcttgctt------------------tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
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---------------------gttggttgttttcgtttgacaagt------------tacatacatgactcttgtcttgcttta-------gGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
atatagcattattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA