Sequence
atgc intronic sequence ATGC exonic sequence...acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttccct---tccttttggtctttctga--tgttg--taattgctaac----------attgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
| || | || | | | |||| || || | | || |||| | || |||| || | || |||| |||| |||||| || | ||||||| ||||| ||||| ||||| ||||||||||| || || |||||||| || || ||||||||||| || |||||||| || ||||| || || || || |
-----gtaaaatgggtg-ttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
---------------acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
| ||| | || |||| | | || ||| |||| | || || | || | || | | | ||||||| ||||| ||||| ||||| ||||||||||| || || |||||||| || || ||||||||||| || |||||||| || ||||| || || || || |
gtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatac-ctgcactctttgg---tgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC-----------------
|||| || | | | ||| | || ||| || || |||||| ||||| ||||| ||||||||||||||||| || || |||||||| || || ||||||||||| ||||||||||| ||||||||||| || || || |
-------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgtgtgcacttttat-gtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
--acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
| | | || | | | || || || || |||| || | | | ||||| || ||| || || |||||| ||||| ||||| ||||||||||||||||| || || |||||||| || || ||||||||||| || |||||||| ||||||||||| || || | |
tgtcataccgtgtttgttgatgcatggatcttactatactttgcc-aatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttat-gtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
---acttggaaaggagtatggtct-aatagttttttcatgctctgtttgatt---tgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
| ||| | || | | | | |||| | | |||| ||| | | ||| ||| || | | || | ||||| | | | ||||| ||||| ||||| ||||||||||||||||| ||||| || ||||| || || ||||||||||| || |||||||| ||||||||||| || ||||| |
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------------------------acttggaaaggagtatggtctaatagttttt--------tcatgctctgtt---tgatttgtgttt-----cccttccttttggtctttctgatgttgtaa---ttgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
| || ||||| || | ||| |||| |||| ||||||| |||||||||||| || | ||| | | | | || | | |||| || | ||||||| |||||||||||||||||| ||||||| |||||||||||||| ||||| || |||||||||||||| ||||| ||||||||||| || ||||| || |
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaat--ccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
------acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttt--tggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
||| |||||| ||| ||| | || | ||||| | | | ||| || ||| | | ||| || | | ||| | | || |||| |||||||||||||||||| ||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| ||||||||||| || ||||| || |
tcaattccttttaaaggaactcattct--ctgttccctgat-ttgtgtttcacacttctatcctttattttcctaatttttacgaggct-----tgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 11
acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaat---tgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
||| | ||| | | | | || || ||||| ||| | ||| || | || ||||| | || || | | ||| | | || |||| |||||||||||||||||| ||||||||| ||||||||| || ||||| || |||||||| ||||||||||||||||||||||| || || || ||||
ccttttttatttccttggaggga-attaaatgtctgttcagtttgctttattttttattt--tgctgatctttttaatcttatgagacatgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTGGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
-acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
|| | ||| || || |||| ||| || |||| ||| || ||||| | | | ||| | ||| | | | |||| |||||||||||||| ||| ||||||||| ||||||||| || ||||| || |||||||||||||||||||||||||||||||| || || || ||||
ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgcatataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
tgctaac putative branch site (score: 1)
ttgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - -gaaagga
- - - - - - - - - - - - - - - - catgctc