Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
| || | | | | ||||| |||| || || | |||| ||||| | | | | |||| | ||| || | || ||||| |||||||| |||||||||||||| || ||||| ||||| ||||| ||| | ||||| |||||||| || ||||| |||||||||||||
----------------------------------------------------------------------------------------gtactgcacatttgaccagaaaaatcctagtcttggactctgaa-attg---cttgcttactcttttattctctgcaatgc----agTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
| | || | | || ||| | ||| | | | | |||||| | | | |||||| | ||| || | |||||||||||||| || |||||||| |||||||| ||||| ||||| ||||| ||||| || |||||| || ||||| | |||||| ||||
----------------------------------------------------------------------------------------gtaatatgcttcctaccattgaagtccaat--ttggattattaaaaatggtctcttatgctcctc----tctgttttatgc----agTTAAGTAGCTGCTTCCTCATCTGCATGAACGATGATAGCATTGAGGGAATTTATGATACTCTCTCAGAATGTGCTACCATAAGCAAATGTGCTGGTGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
| ||| | | | | || || | | ||| || || || || ||| | || |||| || ||| | || ||||| || ||||| |||||||||||||| || ||||| ||||| ||||| || || || ||||||||||| || ||||| |||||||||||||
----------------------------------------------------------------------------------------gtactgtcttgtttcccgccaga------tgatgtcattgtgggttctgaaattgtttatttactgctgctttttctgtgatg-cagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
| | | | || | | | | || ||| ||| || || || |||| |||| || |||| || ||| | || ||||| || ||||| |||||||||||||| || ||||| ||||| ||||| || || |||||||||||||| || ||||| || ||||||||||
-----------------------------------------------------------------------------------------------gtactgtcttgcttcc-tgccagacgatgtcattgtgggttgaaattgtttacttactgt-ttcttttctgtgatg-cagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
||| | | ||| | | ||||| | || | ||| | | || | ||| |||| |||| |||| || || | | | || || | | |||||| |||| | ||||||||||| ||||||||| | |||||||||||||||||||| || || |||||||| ||| | |||||||||||| | |||||||| || ||||||||||
-----------------------------gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgtcttttc--ttgtttgt--aataatgcattag-------tgatttgatgatctg----ggctcttatttaagcgagtgttca--tatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttct-tatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
|| | |||| | | || | | | || | | ||||| || ||| || | |||| || | ||| | | || || ||| | || | | | | || || ||| ||||||| ||||||||| | |||||||||||||||||||| || ||||||||||||||| | ||||||||||| || || ||||| || ||||||||||
----------------------------------------gtatagtttctgttaatgctctttccctccatgtctccctttttttg--tgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttgg-atatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
||| | | |||||| | | | ||| || ||||| || || | | || || || |||| |||| | | | | | | || || | | |||||| | || | ||||||||||| ||||||||| | || ||||||||||||||||| || || ||||| || ||| | |||||||||||| | |||||||| || ||||||||||
-------------------------------gtatgatta---cattttac-catacccttttgaaattatt-atgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctg----gggtcttatttaagcgagtgttca--tgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA---------------------------------------------
|| || ||| ||||||| ||||||||| | |||||||||||| ||||||| || ||||||||||||||| | |||||||||| ||| || ||||| || || |||||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------gtgcattggcagttgagtagttgcttccttgtgtgcatgaaagattatagtatagagGGAATATATGACACTTTGAAGGAGTGTGTTGTCATTAGCAAATCAGCAGGAGGAATTGGTGTTAGTATTCACAACATTCATGCCACAGGCAGTTACATTT
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgtttcacacgcacatgaactagattttatataacttg--tccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
|| ||||| | | ||| || | ||| || | || || ||||||| ||| || | || | ||| | || | ||||| ||| | || || ||| || | | || |||||||| || ||||||||| | |||| |||| || || ||||| || || || |||||||| ||||||||||||||||| |||||||| ||||| ||||
-------------------------------gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttatt--ttgttt--------tacttctt---ccctcttggtgggcggtgta--atggaaggtacttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
||| ||| ||| ||| |||| || ||| | | | | || |||||| ||||||||||||||| | |||||||| || ||||| |||||||| || ||||| || || ||||||||||| || ||||||||||| || || || |
-------------------------------------------------------------------------------------------------------------------gttggttgcttcgtg---attctccttttgtagtttacttctaactgtgacttct-acagCTTAGTAGCTGCTTCCTTCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
||| ||| ||| ||| |||| || ||| | | | | || |||||| |||||||||||||| | |||||||| || ||||| |||||||| || ||||| || || ||||||||||| || ||||||||||| || || || |
-------------------------------------------------------------------------------------------------------------------gttggttgcttcgtg---attctccttttgtagtttacttctcactgtgacttct-acagCTTAGTAGCTGCTTCCTCCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
tgctaat putative branch site (score: 2)
taatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA