Sequence
atgc intronic sequence ATGC exonic sequence...cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttttaatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 1
-cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagtttt---aatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
| || | | || || || ||| ||| | || | | | | ||| | || || | | | |||| | ||||| | |||||||||| || || ||||| || ||||| || ||||||||||||||||||||||| || ||||| || || || || |||||||| |||| |||||||||||
ctatatacttctatttgt---atttctgttctttttattttcgggtgtactgttggatgttattgcttttatgcta-tttactaatagtgttttggtagtgcagATGAAAACTGGCTGTGTGGCACTTGTGTTGTGTTTAAACATTAGTGTTGATCCGCCGGATGTGATCAAAATCTCCCCTTGTGCAAGAAAGGAGTGCTGGA
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 1
----cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttt-taatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
|||| || || | | | | | | | || || ||| | | |||| | |||| |||| || ||| || |||||||||||||||||||||| || ||||| |||||||||||||| ||||| |||||||||||||||||||| || || |||||||| ||||||||||||||||
cttcttcttaatataataccgtgggtggtctttcccctaccggccgagtt--tttttggat-tgtttacatgatcttta--ctaacaatggattttgtagtgcagATGAAGACAGGATGTGTTGCACTTGTATTATGTTTAAACATAAGTGTGGATCCACCTGATGTAATTAAAATTTCCCCTTGTGCAAGAATGGAGTGCTGGA
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
--cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttt-taatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
||| ||| | ||| | | | || | |||||||| | ||| ||| | ||| | || |||| | |||||||| | ||| | |||||||||||||||||||||||||||| || |||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||||||||
ttcctctaaaatgttctaatgattgtttctttaagatgcttatatatta--tatctttggtaag-aagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 1
--cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttt-taatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
||| ||| | ||| | | | || | |||||||| | || ||| | ||| | || |||| | |||||||| | ||| | ||||||||||||| |||||||||||||| || |||||||||||||||||||| ||||| || |||||||| |||||||| |||||||||||||||||||||||||
tccctctaaaatgttctaatgattgtttctttaagatgcttatatgtta--tatctttggtaag-aagtatgctctattttaactcttaactttgtggtgcagATGAAGACTGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCTCCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
----cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttttaatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
| || | | | |||||| |||| || || ||| | || | ||| || || || | | || |||||||||| ||||||||||||||| | ||| | ||||||||||||| ||||||||| || ||||| || ||||||||||||||||| ||||| ||| ||||
tctcgtcggaagctaaatcaggtgttcattggatctgatagctagggga--gttcttgcaagtctcatattctttgttaacttttcttcttcttctt--tgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactc-ccgagttttaatg-cagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
|| | | | | ||| ||| |||| | | | || | | | ||| | ||| |||| |||||||| ||||||||||| ||||| ||| | ||||| |||||| ||||||||| |||||||| |||||||| ||||| || || ||| | || |||||||
--------------------------gttagtttctcctcccaatctatt-ttgttgccactagattgtgtactcttcttgctcactctttttcaatggcagATGAAAACAGGATGTGTTGCTCTAGTTATGTGTTTGCACATTACTGTTGATCCCCCTGATGTTATTAAGATTTCTCCCTGCGCAAGACTCGAATGCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattattgtacgtatttaggtctgctttggtttaactcccgagttttaatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
ttttaat putative branch site (score: 3)
agttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttttaatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - -tcaatca
- - - - - - - - - - - - - gtgcttg
- - - - - - - - - - - - - - - - - - - -acaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactccc