Sequence
atgc intronic sequence ATGC exonic sequence...aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 3
--aat-ttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaatt-ccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
||| |||| | | | | | | | ||| | | | | | | || ||||| |||||| | | |||| ||| | || |||| || || || || | | || |||||||| ||||||||||||||| | |||| |||||||||||||||| |||| || ||||| |||||||| |||||
aaaatgttttgtggtaatcctttttccattatt--aacttcacatctatgatattctgattttccatgctatttgct--tgttatttcctttattcttttgcagGTTTTCCTATACTTGGAATAGAATGGCAGAAAATGGAAAATCCTGATCTCCGAAAGGCAATGGGAATGAAATCTGACCAAAAGGGTGTTCGTGTCAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 3
-aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgat--atttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | | | | | | || | | || | || ||| || | | || | | | || ||| || | ||| ||| | || |||||||||| || || | | || |||||||| ||||| ||||||||| | || | || |||||||||||||||||||| ||||| ||||||||| ||||
cagtctatggttaccacttctatct--ttctggtattttacatttgccacgtggttttttgaaggttccgttatttaatatcttcatgtattata-atttcagGATTCCCTATACTTGGAATAGAATGGCAGAAAATGGAGAATCCTGATCTCCGCAAAGCGATGGGAATGAAACCTGATCAAAAGGGTGTTCGTGTTCGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G144501_T02 (Zea mays), 3'ss of exon 3
aatttttcccttgctttatgatgtaatgctcaaaccttttttttc--ccctgcttctaattccatgatatttgttatcatgattttgtt-ttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | | ||| | ||| ||| | | ||| | || | | ||| | | | |||| | | | ||| | || || || | | || |||| || || || ||| | |||| |||||||| ||||| ||||||||| | || | ||||||||||||||||| ||||| ||||| ||||||||||| ||
--tccatgtaatacttagtactgtgatgttgatgcctatcccttagatctttcttattttccaatgacagcc-taaccatattctttttgtttattatttcagGGTTTCCTATACTAGGAGTTGAATGGCAGAAAATGGAGAATCCTGATCTCCGTAAAGCAATGGGAATGAAACCAGATCAAAAGGGTGTTCGTGTTAGGAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 3
aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattcc--atgatatttgttatcatgattttgtttta-aatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | || || | | | ||| ||| ||| | || |||||||| | |||| | | |||| || | || || | | | || ||| || || || || | |||| |||||||| ||||| ||||| ||| | || | ||||||||||||||||| ||||| ||||| ||||||||||||||
-ctccatgtaatgtttagtactatgatgttcatgcctacctcttagatc-tttctaatttccaatgacagt-gttactatattctttttatgtattattttagGCTTTCCTATACTTGGAGTTGAATGGCAGAAAATGGAGAATCCAGATCTCCGCAAAGCAATGGGAATGAAACCAGATCAAAAGGGTGTTCGTGTTAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 3
----aatttttcccttgctttatgatgtaatgctcaaaccttt----tttttcccctgc--ttctaattccatgatatttgttatcatgattttgttt---taaatgtt-ccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
|| | | | || |||||| ||| | | | || || || || | | | | || ||| ||| ||| || || | ||||||||| || || | ||||||||||||| ||||||||||||||| |||||||||| ||||| ||||||||||||||||| || || || |||||||
gtaatatggtagctaggaactaagatgtagatttcacttttacaagatgctacctgagcatttttagaattaagttttatgcactcagatctttctttctctatctgctgttagGATTCCCTATTCTTGGGGTTGAGTGGCAGAAAATGGAAAATCCTGATCTGCGAATGGCCATGGGCATGAAACCTGATCAGAAAGGTGTGCGCATTAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 3
----------aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgtttt----aaatgtt-ccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | || | ||| | | | | | | | | || || | || | ||| || ||| | || | ||||||||| || || | |||||||||| || ||||||||||||||| |||||||||||| ||| ||||||||||| ||||| || || ||| |||||||
gtaatatggtagctacaaactaagatgtagatttcacttttacaagatgctatcagagcatttttagaattgaagttttatgcactgagatctttctttctcaatctgctgttagGATTCCCTATTCTTGGGGTTGAGTGGCAAAAAATGGAAAATCCTGATCTGCGAATGGCAACGGGCATGAAACCTGACCAGAAAGGTGTGCGTATTAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 3
aatttttcccttgctttatgatgtaatgctca--aaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
|| | | | | | | || || ||| | || |||| |||| ||| || |||| || || |||| ||| || || | || | |||||||||| ||||||||||||||||||||||| | | ||||||| ||| || || |||| ||||| || || |||||||
---------------gtaagtttcaccgatgattaatgttgtttgttatctatctcta----catgtgcttttttctcata------cttgaactgttttagGGTTTCCTGTTCTCGGAATTGAGTGGCAAAAGATGGAAAATCCTGATTTGCGGAAGTCAATGGGTATGGAATCTCATCAAAAGGGAGTGCGGATTAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ16952 (Selaginella moellendorffii), 3'ss of exon 3
aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | || | | | | || ||||| | | | |||| || |||| |||| || |||| || || || || || | || |||||||||||||||||||| |||||||| | |||| | || ||| ||| ||||||| || ||||| | |||||
----------------------------gtaatactgtcctgtagtcttgattctagctgcgttctattc-tttccatgttttttttg---------cagGGTTTCCCATTCTTGGCGTGGAATGGCAGAAGATGGAAAATCCGGATTTGCGGAAGGCAGTCGGGATGGCACCGAATCAGAAAGGTGTTCGCATAAGAAG
upper sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ16073 (Selaginella moellendorffii), 3'ss of exon 3
aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
| | || | | | | ||||| | | | |||| || |||| |||| ||| |||| || || || || || | || |||||||||||||||||||| |||||||| | |||| | || ||| ||| ||||||| || ||||| | |||||
----------------------------gtaatactgtcctgtagtttagattctagctgcgttctattc-tttccatgtttttttttg--------cagGGTTTCCCATTCTTGGCGTGGAATGGCAGAAGATGGAAAATCCGGATTTGCGGAAGGCAGTCGGGATGGCACCGAATCAGAAAGGTGTTCGCATAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
ttctaat putative branch site (score: 2)
atatttgttatcatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttttcccttgctttatgatgtaatgctcaaaccttttttttcccctgcttctaattccatgatatttgttatcatgattttgttttaaatgttccagGATTCCCAATCCTATGCCTTGAGTGGCAGAAGATGGAAAATCCTGATTTGCGAATGGCAATGGGAATGAAACCTGATCAGAAGGGCGTTCGTGTTAGAAG
- - - -cccttgc
- - - - - - - - - - - gtaatgc
- - - - - - - - - - - - - - - caaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatt