Sequence
atgc intronic sequence ATGC exonic sequence...ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
--ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
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aatgttggtaatacttttagagcttgctttgattttgttcatt--gctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattga-taccaatctattttcttgacatctttgtt----tctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
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----gatgatgtatagcatatccaccaagaaccacca-tataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G432083_T01 (Zea mays), 3'ss of exon 3
ctttcataactct-tgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttg-acatct--ttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
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---tcttgattcaatgctgggacaaagtactttttgttgttctagt-gttcaaccaaaacaaactaacgccaacaaactgacttgcatgttgaatgacctatagGGTGGTGGGCCATATTATCTTATAGGCCGTGCACTTGGTCCTGAAGTTGGAGTTAGTATAGGATTATGCTTCTTCCTCGGGAATGCAGTGGCTGGATCCA
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
----ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttg-tttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
| || ||||| | | | || | | || | ||||||||| | | || | | || | | || | | ||||||||||| || || |||||||| || |||||||||||||| |||||||||||||||||||| ||||| || ||||| || ||||| || || ||| | |
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcatt----aataattgatat-agtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
ctttcataactcttgttttactggcttaggc--ttccttctttttgttgtcctttttgtattaattgatacca--atctattttcttgacatctttgtttc-tagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
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-----aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------------ctttcataactct-tgttttactggcttaggctt------ccttctt--tttgttgtcctttttgt-attaattgataccaa-----tctattttcttgacatcttt---gt--ttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
|| || | ||| || | |||| | || |||| || ||| | | |||||| ||| | | || | || | ||| || | | |||| || | ||||||| || |||||||| ||||||||||| || |||||||| |||||||| ||||||| || |||| || || ||||| |||||||| |||||| |||
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S5_444V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaa-----------ttgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
|| || |||||||| | | | | || || | | || | |||| | | | || | ||| | || | | || ||| | || |||||||||| || ||||| || || ||||| || ||||||||||| |||||||| || |||||| | ||||||||||| || |||||||| |||| |||
gttagtatcttgagtaaaggaatttcatgtgtcgaaattcaatcaatcatgtatttgcaatactcttgtctcaaggacatatgcatgtaaatcatttaaggactttatatttgaagcagtttgtcttccataagattccaacgttttatcattct--attacagGGTGGGGGTCCCTATTACCTGATAGGTCGGGCTCTTGGTCCAGAGGTTGGAGTAAGTATTGGATTGTGTTTCTTCCTGGGCAATGCAGTTGCTGCATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcctttttgtattaattgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
tctttgtttct CT-rich tract
tttttgtattaattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - -ttactgg
- - - - - - - - - - - - - - -gcttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataccaa