Sequence
atgc intronic sequence ATGC exonic sequence...tttaccttcttccctatttgatcatatctcactgctatggtaaatgacttgtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 4
-----tttaccttcttccctatttgatcatatctcactgctatggtaaatgacttgtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
||| || ||| |||| | | || || | | |||| | | | ||| || | | | | |||||||||||||| || ||||||||||| ||||||||||| || |||| | ||||| ||| | || ||||||||||| |||||||| ||||||||||| ||
caacctttggtagaacccacattgatatatatatatatatatatatatatatatatatatatatatatatatatattttgctactgttggaa-----taattcagGTCTTCCCCGAAGCGAATTGAAGGTCCTGATGGAAGAAATCTGCAACTCCAGTTCAGGACAAGACTGTCTCTTCCTCTTTTTACTGGAGGAAAAGTTGAA
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 4
-tttaccttcttccctatttgatcatatctcactgctatggtaaatgactt--gtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
| | | | |||| | | ||| ||| | | || | | | | |||| | | |||||| | | || || |||| ||||||| || ||||||||||| || ||||||| | |||| | | || | | |||||||| |||||||||||||| ||||||||||| ||
ataaatcattttccttcacttgccat-tctgagtagattgcaatccaaataaggaatcatgttgatgctaacaattttttcctctc--cttttaatataacagGCCTTCCCCAAAGCGAATTGAAGGTCCAAATGGAAGAACTCTGCAACTCGAATTCCGAACAAGGCTGTCACTTCCCCTTTTTACTGGAGGAAAAGTTGAA
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G07290.2 (Glycine max), 3'ss of exon 5
-tttaccttcttccctatttgatcatatc-tcactgctatggtaaatgacttgtttcatatctggcttggtggttttttatttctaacaatt--gccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
| || | | || || || | | | || || | || | | || | | | |||| ||| || | |||| || ||| ||||||| | |||||| |||||||| |||||||| || | ||||||| || | ||||||||| || ||||||||||||| || |||||||||||||| ||
atgtaaactgtcaccacttcaatgccaccataacatctgttgtttaaatttagtacctcagtgagtctggtattttcttgt----aacagtttaaaaattccagGTCTCCTCCTAAAATGATTGAAGGCCCTGATGGTAGAAGCTTGCAGCTGAAATTTAGGTCCCGGTTGTCTCTTCCCCTATTCACAGGAGGAAAAGTGGAA
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 4
-tttaccttcttccctatttgatcatatc-tcactgctatggtaaatgacttgtttcatatctggcttggtggttttttatttctaacaatt--gccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
| || | | || || || | | | || || | | | || | | | |||| ||| || | ||| || ||| ||||||| | |||||| |||||||| |||||||| || | ||| ||| || | ||||||||| |||||||||||||||| || |||||||||||||| ||
atgtaaactgtcaccacttcaatgccaccataacatctgccatttaaatttagtacctcagtgagtctggtattttcttgt----gacagtttaaaaattccagGTCTCCTCCTAAAATGATTGAAGGCCCTGATGGTAGAAGCTTACAGCTGAAATTTAGGTCCCGGCTGTCTCTTCCCCTATTCACAGGAGGAAAAGTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacttgtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
ttctaac putative branch site (score: 1)
ccatttc putative PPT
ttttttatttctaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaccttcttccctatttgatcatatctcactgctatggtaaatgacttgtttcatatctggcttggtggttttttatttctaacaattgccatttcagGTCTTCCCCTAAACGAATTGAAGGACCTGATGGAAGGAACTTGCAGTTGCAGTTTAGGTCCAGGCTGTCTCTTCCCCTTTTTACAGGAGGAAAAGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - -tcttccc
- - - - - - - - - - - - - -ctcactg
- - - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaatt