Sequence
atgc intronic sequence ATGC exonic sequence...gtacaacagctaattcaacatctatcaagttaacaacacattaatagaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g67570.1 (Oryza sativa), 3'ss of exon 4
gtacaacagctaattcaacatctatcaagttaacaacacattaatagaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
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gtatggtttcttgttctga---tatacaattgtggac---ctggtatacttatttgtgaaagaattctgcgtgccatttacatctcattatttgttt-agGTGGGTACCAATAAAAGGAAATGATTGGTATTGGATCCGTCATCACATCAGACCTGGCATGGAAGTCCATGTAGAGATTCTG
upper sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G18080.1 (Glycine max), 3'ss of exon 4
-gtacaac-agctaattcaacatc-tatcaagttaacaacacattaatagaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
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agcatatttatcttgttcagtgttactttttgatgtttatatttttatgcgagtgttcttctgt---tcttctggaagattcatctaccatgttgtgttctagGTGGGTTCCTATAAAGAACAATGATTGGTATTGGCTTCGCCATCACATAAAAGTGGGTATGCACGTCATTGTTGAAATTACG
upper sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G36900.1 (Glycine max), 3'ss of exon 4
-gtacaacagctaattcaacatctatcaagttaacaacacattaatagaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG------------------
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gcttttgtagcatatttatcttgt-tcagtgttactatttgatgtttatatttttatgcaaatgttcttctggaagattcatctaccatgttatgttctagGTGGGTTCCTATTAAGAACAATGATTGGTATTGGCTTCGCCATCACATAAAAGTGGGTATGCACGTCATTGTTGAAATTACGGTGAGTGTTTCAGTCAGT
upper sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G48500.2 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------gtacaacagctaattcaacatctatcaagt-taacaacacattaatagaaatcatatttcaaatatttcatgc--------ttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG------------------
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gtatgtttatgtctctttactttgtaaagatagacttaccgtggttcttgtatttagggtatataacgtaatataatgttgtctcttgtttcatatgctttttttgaaagatgtaagtttatgtgtct-attggtttgcagATGGGTACCTATAAAAGGTAATGACTGGTTTTGGATCCGGCATTTCATAAAAGTTGGGATGCATGTTATCGTTGAAATCACGGTAATCTTAAGGCACATA
upper sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G48500.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------gtacaacagctaattcaacatctatcaagt-taacaacacattaatagaaatcatatttcaaatatttcatgc--------ttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
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gtatgtttatgtctctttactttgtaaagatagacttaccgtggttcttgtatttagggtatataacgtaatataatgttgtctcttgtttcatatgctttttttgaaagatgtaagtttatgtgtct-attggtttgcagATGGGTACCTATAAAAGGTAATGACTGGTTTTGGATCCGGCATTTCATAAAAGTTGGGATGCATGTTATCGTTGAAATCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
gcttgat putative branch site (score: 5)
tcttgttttgtttc putative PPT
atatttcaaatatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaacagctaattcaacatctatcaagttaacaacacattaatagaaatcatatttcaaatatttcatgcttgattcatgtatcttgttttgtttcagGTGGGTCCCTATAAAAGGCAATGATTGGTATTGGATTCGCCACCACATAAAAGTTGGTATGCATGTCATTGTTGAAATCCTG
- acaacag
- - - - - - - -caacatc
- - - - - - - - - - - - - - - - -caacaca
- - - - - - - - - - - - - - - - - - - - - aatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgta