Sequence
atgc intronic sequence ATGC exonic sequence...tgaaaaatatgcagcttcccacttacatgtttgtggttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 4
tgaaaaatatgcagctt-cccacttacatgtttgtgg-ttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
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tgattttcctttagtgaactcaacatgatgatgatgaatttgccttacagtaaattttccatagaacttgt--tttttcttatggtaagtttgccttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGATTTCAAGTGTCATGAAGGCCAGATTCAGTGCATAGATTTCCATCCCCATGAGTTCCTTCTGGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 4
---------------------------------------tgaaaaatatgcagcttcccacttacatgtttgtgg--ttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
|| | | | | ||| | | | | | | | |||| ||| | || || || |||| | || | || | | | | | ||||| |||||||| || ||||||||||| || || || ||||| |||||||||| ||| | |||||||||||||||||||| ||||| || || |||||||
gtaataatttaccagtaactcagtgctgtgtgtttcaattgctagtttttctgctggaatttgatttttcttttgccttaatctttgtaatgaaaaattcttattttttggaactcgtcacaatatgctttgccttggcagCTCTGGGATCTTACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTTCATCCCCATGAGTTCCTCCTGGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 4
----------------------------------------tgaaaaatatgcagcttcccacttacatgtttgtgg--ttaaccttgtaagtg-----tttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
|| | | | | ||| | | | | | | | |||| || | || | || |||| | ||| || | |||| | | ||| ||||| ||||||||||| ||||||||||| || || || ||||| |||||||||| ||| | |||||||||||||| || || || || || || |||||||
gtaagaatttgccaataactctatgctgtgtgtgttcaattgctagttcttctgctggaatttgatttttcttttgccttaatatttctaatgaaaaaaatcctttttttcccgaacatattac-aatatgtt--tttctttggcagCTCTGGGATCTGACAGCTGGAAAGTTATTACATGAATTCAAGTGTCATGAGGGTCAGATCCAGTGCATAGATTTCCACCCCCACGAGTTCCTTCTGGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 5
tgaaaaatatgcagcttcccacttacatgtttgtggttaaccttgtaagtg-----tttttttgttttttt-------aatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
| | || ||| |||| |||| || ||||||| || |||||| ||||||| ||| || | ||| | || | ||| | |||||||||||||| || || | ||||| ||||| ||| |||| ||||||||| | || || |||||||||||||| |||| ||||| || ||||
----------gtaaatttg-gcttgcatggttgta-ctacacttgtaaatgaggaccttttttttttttttggaaaaaaatgatgtaaattatagtgtatatatgtttgcagTTATGGGATCTGACTGCGGGGAAACTCTTGCATGATTTTAAATGTCACGAGGGCCAGGTCCAATGTATAGATTTTCATCCCAATGAGTTTCTACTAGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 5
tgaaaaatatgcagcttcccacttacatgtttgtggttaaccttgtaagtg--------tttttttgtttttttaatcatct-tgccaat-aaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
||| | || || ||| ||||| ||| ||||||| || ||||||||||| || || || ||| | ||| || | ||| | |||||||||||||| || || | ||||| ||||| ||| |||| ||||||||| | || || |||||||||||||| |||| ||||| || ||||
--------atgtaaatttg-gctcgtatggttgtg-ctaaacttgtaaatgagaacctatttttttgtttggaaaaaaattgatgtaaattatcatgtatatgtttgcagTTATGGGATCTGACTGCGGGGAAACTCTTGCATGATTTTAAATGTCACGAGGGCCAGATCCAATGTATAGATTTTCATCCCAATGAGTTTCTACTAGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 5
--tgaaaaatatgcagcttcccacttacatgtttgtggttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactac-ttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
|| | | | | | || | | |||||| | || | || | | | | || | | | | ||| | | | |||| ||| |||||||| ||||||||||||| | ||||| || || || |||||||| || | ||||| | ||||||||||||| |||||||||||||||||||
tttgtactgtttaccgtaattgttttcctgaaaagcaagtaacct-gcaaattttgctctctctcttaa--cgttggactgatatgtgggttgccttcaccagGTGTGGGATTTGACTGCTGGAAAACTTTTGCATGAGTTTAAGAGTCATGAAGGGAAAATTCAGAGTCTAGATTTTCATCCCCATGAATTTCTGCTGGCAA
upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G23430.1 (Arabidopsis thaliana), 3'ss of exon 5
-tgaaaaatatgcagct-tcccacttacatgtttgtggttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
| | | | | | || | ||| | |||||| | | | ||| | | ||||| || | | | ||| | ||| | |||||| | || |||||||| || || ||| || || |||||||| || || |||| || |||||||||||||||||||||| || |||||||
cagcgcactgtattgttatcttgaaaagcaatttaccgggaacctttttttttatctttctgtgtgttaatggatctgatatgcagcttgt--ctttaccagGTTTGGGATTTAACAGCTGGAAAACTGCTGACCGAGTTTAAGAGTCATGAAGGGCAAATTCAAAGCCTAGATTTTCATCCTCATGAATTCCTACTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
ttttaat putative branch site (score: 3)
ctacttc putative PPT
tttttttgttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaaaatatgcagcttcccacttacatgtttgtggttaaccttgtaagtgtttttttgtttttttaatcatcttgccaataaaatgactacttcaacagCTGTGGGATCTGACTGCTGGAAAGTTGTTGCACGATTTCAAAAGTCATGAGGGCCAGCTTCAGTGCATAGATTTTCATCCTCATGAATTTCTGCTGGCAA
- aaaaata
- - - - - - - -ttcccac
- - - - - - - - - - - - acatgtt
- - - - - - - - - - - - - - - - - - - - ccttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa