Sequence
atgc intronic sequence ATGC exonic sequence...taatagtatttatgaaattctaaaaaatctagtgccatgtgtctctgattactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 5
----taatagtatttatgaaattctaaaaaatctagtgccatgtgtctctgattactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
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agccgactagcctctttaatatctctgctgttcaaatactttaaaggtttacgttccg---gttctgagcttgggatttctgctattatgcctat-ctgtgcagATTAATGACCGCTATGAATTCCCTTTGCAACTTGATTTGGATAGAGATGATGGAAAATATCTTGCTCCAGATGCAGATAGAAGTATAAGAAACCTTTATG
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 9
taatagtatttatgaaattc-taaaaaatctagtgccatgtgtctc---tgattactgt--atacttcatctttttcctagcaat-aataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
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-------aattaagtaattaacgtgatatctatcctcttatttctcatataataattatggaaagttcagcaacaaatcgttgattgattaacgtccaattctgcagATTAATGACCGGTATGAGTTCCCACTTCAACTTGATCTTGACAGAGATGATGGGAAATATCTTGCTCCTGATGCAGATAGAAGCATTAGAAACCTTTACA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 9
-------taatagtatttatgaaattctaaaaaat---ctagtgccatgtgtctct--gattactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
| | || | || ||| || | | | |||| ||| | | || ||| | | | || || | || || ||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| |||||||||||| | || || || |||||| | ||| || | ||||| || |
gttagaaccgtgctgaataccaccatccaaatgataaaccacttccatacatcttaagaaatggtgaataaggttacccaggattggtgatgatcttatctac-ttctgcagATTAATGACCGCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 5
taatagtatttatgaaattctaaaaaatctagt---gccatgtgtctctgattactgtatacttcatctttttcctagcaataataatggcttt-gttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
| | | | ||| | | || | | | ||||| || | | | | | | | ||| | | | | | ||| || || ||||||||||||||||||| ||||| |||||| | || ||||||||||| ||||||||||| | || || ||||| ||||| ||||| || ||||| || |
----ggatatcactatcatctgagacatgcattcaaaatacttgtctatggctgatttgcattcttgcgtcttctaaattaaattgtttttttttgtgatgtagATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTTCTCCAGACGCGGATAGAAGTGTGCGTAACCTATATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 9
taatagtatttatgaaattctaaaaaatctagtgccatgtgtctctgat-tactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
|||||||| ||| | | | | | | | || | | | | | ||| || | || | ||| ||| |||||||||| || ||||| || || ||| |||| || ||||||||||| ||||||| ||| |||| ||||| || || |||||||| ||||||||||| |
-gttagtattt--gaagtcacatgtacataggaagtgaatatgtggtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattg-atagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------taatagtatttatgaaattctaaaaaatctagtgc---catgtgtctctgattactgtatact-------------tcatctttttcctagcaat--------aataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
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gtgaggaaaggggttttcgaaccatgcaatatgcaacattcggctggtatagcttatgtattgattgtgcatattatttagatgaaggacgtgtgtgtgtgtgtgtgtgtatttgctttgttttggttggttggtagtcacttttttactactgattacctttgaacattatttatgtgatgcagATTAATGATCGCTATGAGTTTCCTCTGCAACTAGACCTGGATAGAGAGAATGGAAAATATCTCTCTCCTGATGCTGACCGCAGTGTGCGAAATTTATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
ctctgat putative branch site (score: 4)
ctttgtt putative PPT
aataataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatagtatttatgaaattctaaaaaatctagtgccatgtgtctctgattactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatggct