Sequence
atgc intronic sequence ATGC exonic sequence...ctagaaaaagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
-ctagaaaaagttacaaat-cttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------
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gtatgaaagacacagaaatgcttcaacctgt------gcgatttttttatcgtattgttatttgacaactaactaacta-accatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
upper sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 4
ctagaaaaagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------
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-----gtagttcctagatacgccatttgtttccaacagtaccatatatactagtgt-attagaattaactatccctt---ttatcttcacatg-atatagGCATATGACACAATGGTGGGTCAACATGGTGCTCAGCTTTCTGGGGGACAAAAGCAAAGGATTGCCATTGCAAGAGCTATCCTTAAAAATCCAAAAGTCC
upper sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------ctagaaa-aagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------
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gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagc-atttatttcatcttaatttg--gggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
upper sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 5
--------ctagaaaaagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatgg-ttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------
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gtataactcaatgaactattacgtccgtaatgctatttatttattatatagatgctaattttct-gccactcccattgttaatcagtacatcttgtgaaacatccgcagGGTCTTGACACAATGGTGGGGGAACATGGAACTCAGCTGTCTGGAGGGCAGAAACAGAGAATAGCAATTGCTAGAGCAATCATAAAGAACCCTAAGATCT
upper sequence: Vv00s0388g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G086730_T01 (Zea mays), 3'ss of exon 6
ctagaaaaagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT-------------------------------------
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----------gtacatataaactaatg--cggtcataatattaaccttttttttttgccacagatt---attaaccagtatattttgtgaacat-tacagGGTCTTGACACATTGGTTGGGGAACGTGGAACTCAACTGTCTGGAGGACAGAAGCAGAGAATAGCAATTGCTAGAGCAATCGTAAAGAACCCTAGGATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT
ttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagaaaaagttacaaatcttctgtttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTTGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- agaaaaa
- - - - - - acaaatc
- - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - -gagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg