Sequence
atgc intronic sequence ATGC exonic sequence...agtgacattacaacaaagaatgcaaagcatatttggactctttgttgattttttctaccaatcattattgatttttcttttctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 19
agtgacattacaacaaagaatgcaaagcatatttggactctttgttgattttttctaccaatcattattgatttttcttttctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
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----------------gtgattctcttcac-ccaggacctactgagtacttagt-tacttacgagtacttacgactttgtgcttcatg---atattgcagATTATTGTCGCCACAGACATAGCAGAGACCAGCATTACAATTGATGATGTAATTTATGTAGTTGATACTGGGAAGCACAAGGAAAATCGCTATAACCCGC
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 19
agtgacattacaacaaagaatgcaaagcatatttggactctttgttgattttttctaccaatcattattgatttttcttt---tctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
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--ccacaagtgagctaaagtggtctaaagttttagtccttaactttaaccaactaaacttgagaccagagaatccaaacaggactttcatgt-tgtgttgcagGTTATTATTGCCACAGACATAGCAGAGACCAGCATTACAATTGATGATGTAGTATATGTAGTTGATACTGGAAAGCACAAGGAGAACCGTTATAATCCAC
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G58050.1 (Arabidopsis thaliana), 3'ss of exon 20
----------------------------------------agtgacattacaacaaagaatgcaaagcatatttggactctttgttgattttttctaccaatcattattgatttttcttttctatgtgtatatgt-cccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
| | | | | || ||| || || | | || | | | | | || | || | ||||| ||||| | | ||| |||||||| ||||| ||||| || || || ||||| ||||| || || |||||||| |||||||||||| ||||||| || ||||||||||| ||||| ||||
gtaatatagttaaaagagtttcttgagttatcttcttttaaataagctgataataaactctg-aatgaaaatataatgtttaacaaaagaatgcctgcaaagccgatctgattcgccttttgcgttgtcttttgtattcagGTTATCATAGCTACAAATATTGCCGAGACCAGTATAACAATTGAGGATGTGGTTTATGTGATTGATAGTGGAAAACACAAGGAAAATCGCTATAACCCAC
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G58060.1 (Arabidopsis thaliana), 3'ss of exon 20
--agtgacattacaacaaagaatgcaaagcatatt-tggactctttgttgattttttctaccaatcattattgatttttcttttctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
||| | | | | | | | | ||| | | || | ||| | || | || | |||| | ||||| | || | | |||||||| ||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| |||| || || ||||||||||| || |||||||
ttcttgaaagttgtattatgtgtatataatatacagtaaaggctgcatggatct---ctgcaaagctgatctgatatatctttgcatcgtctcttatgttcagGTTATCGCAGCTACAAATATTGCAGAGACCAGTATAACAATTGATGATGTGGTGTATGTGATTGACAGTGGCAAACACAAGGAAAATCGCTACAATCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattttttctaccaatcattattgatttttcttttctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
tattgat putative branch site (score: 3)
aatcattattgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgacattacaacaaagaatgcaaagcatatttggactctttgttgattttttctaccaatcattattgatttttcttttctatgtgtatatgtcccagGTTATTATAGCCACAAACATAGCAGAAACCAGCATAACGATAGATGATGTGGTGTATGTGATTGATTGTGGAAAGCATAAGGAAAATCGTTATAATCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - -caaagaa
- - - - - - - - - - - caaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatca