Sequence
atgc intronic sequence ATGC exonic sequence...tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 1
tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGG---AAAGGGAAAATTAAGCAG--ATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC
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taagtttccatgtgttccttaatttagtcatagaacacaattcaaccttgtaacaaggtt--atcctggttgatttctgactgttaaatatatttggtaaagGCTAATGGGAAAACAAAGCGGCCTTCTATTTTATTTCCTTCTGCTGCCAGAAGAATGGATACTCTCAATGATTTATTGACAGCAAGTGATCTTGTTTCAC---
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 1
tttgcatctaaatgtgttttgaccagca-tatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtc-----taaaccaaccatttaacagGGAAAGGGAAAATTAAGCAG--ATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC
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----cttcatggtgtttctgggttactggcacatgtaatattggcgat-gaagttaaagcatgatatagatctgaccttgttaattgtaatgacattatgtgaagGTTACTGGGAAAGTAAAGCGTCCTTCTATTGTATTTCCTTCTGCTGCAAGAAGAATGGATACTCTCAATGATCTATTAGCAGCAAGTGATCTAGTTTCGC---
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 1
-tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtcta-aaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC------------
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atttccattattcttttgtttctttggaacatactaatcccaaacagctgactgg-atactatatttttggctaattttgtcttcaaccttgcactca-cagGAAAAAGGAAAAGTAAA------------GTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTACTAGCTGCAAGTGATCTTATATCACTACATTGTGCTTTAA
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 1
-tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC------------
||||||| | | | ||| | | ||| ||| ||| | | | ||| | | | |||| | |||| || | | |||||||| |||||| ||| || ||||| || || ||||||||||||||||| ||||||||| | ||||||||||||||| | || || |
atttgcatttttcttttgtttctttggaacatactaatcccaaacagctgactggattctatatttttggctaattttttcttcaaccttacactca-cagGGAAAAGGAAAAGTAAA------------GTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC
gtctaaa putative branch site (score: 3)
attgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC
- -gcatcta
- - - - - - - - - - -accagca
- - - - - - - - - - - - - - - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccaa