Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatctttcttctttctgaatattgcagtgtccaatgttccctctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 9
------------------gtaagttcatctttcttctttctgaatattgcagtg-tccaatgttccctctctaattctataacatgaatt------tcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
| | | || | || | | || |||| || || | |||| || ||| | | || |||||| |||||||||||||||||||| || || ||||| ||||| || || || || ||||||||||||||
tttattccggtaaccatagaagctgtttcagtgttttgcaacagtaagtcagtactcttatacttcctcagtagggctaacatactgatcaaattatcagGTACTTTTCAAGCTTGTTGTGATAACTGTGCTTGTTATTGCTGAATCCGCCGACAACTGCATAAAAACT
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G081907_T01 (Zea mays), 3'ss of exon 5
-------------gtaagttcatctttcttctttctgaatattgcagtgtc----caatgttccctctctaattcta---taacatgaatttc--agGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
|| | || || ||| | || ||||||| |||| | | | | || | || | | |||||||| | ||| ||| ||||| ||| | ||||||||||| ||||||||||||||||| |||||| |
gtatggtgttcctttatctctatgcatcctctgctaacagctttcagtgtcagactgatgtatctgaatcgaccttgtttttacttaaaatccacagGTCCTTCTTAAGAATGTCGTGATCACCATCCTTGTAATTGCTGAGTCTGCTGATAACTGTATAAAAGAG
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 8
gtaagttcatctttcttctttctgaatattgcagtgtccaatgttccc----tctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
|||||||| || | | ||| || | | ||| | | ||||| | | | ||| |||||||||||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||||||
gtaagttcgcctagttatctcggatttatcacaat-tttgatgcttttgaaattattaatttt-tgatctgataatcagGTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACG
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 8
gtaagttcatctttcttctttctgaatattgcagtgtccaatgttccc----tctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
|||||||| || | | | ||| || | | ||| | | ||||| | | | ||| |||||||||||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||||||
gtaagttc-tcctagtatctcggatttatcacaat-tttgatgcttttgaaattattaatttt-tgatctgataatcagGTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACG
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 8
gtaagttcatct--ttcttctttctga-----atattgcagtgtcca-atgttccct--ctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
|||||||| || || || | | ||| || || || | |||| | |||| | | | ||| |||||||||||| ||||| ||||||||||| || |||||||||||||| ||||| || ||||||||||||| |
gtaagttctactactttttgtctatgataatcatgttttggtttttggatgtatctgaactcttgatacttgatctgataatcagGTCCTTTTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCGGACAACTGCATAAAAATG
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 8
gtaagttc-atctttcttctttctgaatattgcagtg----tccaatgttccct--ctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
||||||| | ||| ||| | ||| || || | ||||| | ||| | | | | ||| |||||||||| | ||||| ||||||||||| || ||||||||||| || ||||| ||||||||||||||||||
gtaagttttactttttatctatggtaatcatgttttggtttttggatgtttctaaaatcttaatacttgatctgataatcagGTCCTTCTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCGGAATCTGCAGATAACTGCATAAAAACG
upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagttcatctttcttctttctgaatattgcagtgtccaa------tgttccctctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
||||| | | | | || | | | || | | | ||| || |||| | | ||| |||||| ||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||||||||||
gtaagcttaacctcctgtcgttt-actactatggcattcaacacatacacattcttgttaatattggtatatggtaatcagGTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgaatattgcagtgtccaatgttccctctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
ctataac putative branch site (score: 3)
taattctataacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatctttcttctttctgaatattgcagtgtccaatgttccctctctaattctataacatgaatttcagGTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT