Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaatgcacaatctattgactaaagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 2
gtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaa-----tgcacaatctattgactaaagttggacatgcttctt-tttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
|| ||| || || | | ||| | || || | | ||| || | || | | | | | | || ||||| || | ||| || || | ||||| ||||| || || |||||||| || ||||||||||||||||| |||||||| || || | || |||||||| | |||||||
gtgagtaccattttttctttcactaattctgtgtcttagactgctcattgtggttggtctttctgggtcagttaatagtttacgataaa-atatttcttgttatgtagTATCGGATGCTTGGCTCGCGAACCCGGCCTTGCCTGAGGACATTCTGAAGGAGGCTGTACCAGGAAACATCAGGAGGGCTGAGCATTTTCTTGCTGTTTT
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 3
gtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaatgcacaatctattgacta--aagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
||| || | ||| | ||| || || ||| |||| || || || |||| ||| | | | || | || | || ||| || || | | || |||||||||| ||||| || |||||||||||||| || ||||||||||| || ||||||||||| || || |||||||| | ||||||
gtatgtaggatg----agagt-----tttgttcttaatgtcttaa-----ttcttaaatgttacctctggtcatcactaactaaaacttcttttctttacgtagCTACTGATGCCTGGCTTGCAAATCCAGCCTTGCCTGATGATATACTAAAGGAGGCTGTACCTGGAAATATTCGCCGGGCTGAGCATTTTATTCATGTTTT
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 3
gtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaatgcacaatctattgacta--aagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
||| || | ||| | ||| || || ||| |||| || || || |||| ||| | | | || | | | || ||| | || | | || |||||||||| ||||| || |||||||||||||| || ||||||||||| || ||||||||||| || || |||||||| | ||||||
gtatgtaggatgtc----agt-----tttgttgttaatgtcttaa-----ttcttaaatgttgcctctggtcatcactaactaaaatttcttttctttacatagCTACTGATGCCTGGCTTGCAAATCCGGCCTTGCCTGATGATATACTAAAGGAGGCTGTACCTGGAAATATTCGCCGGGCTGAGCATTTTATTCATGTTTT
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaatgcacaatctattgactaaagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
|||||| || | | | || | | | | | | || ||| | | | | ||||| ||| | || || ||||| |||| || |||||||| || ||||| ||||| |||||||||| ||||||||||| || || |||||| | || || |||||||| || ||||||
gtaagtatg-tgt-tcaggaaggtgatctgtgatttgattgaaagcacacagtaaattttctaattctatgaacttgacgcaacaat--tttttttttgcagGAGGTGATCAATGGCTTGCAAACCCTGCACTGCCTCATGATATTCTAAAGGAGGCTGTCCCGGGGAATATTAGACGGGCTGAGCATTTTGTGCATGTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttttgaatgcacaatctattgactaaagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
gactaaa putative branch site (score: 2)
catgcttctttttc putative PPT
aatctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggaatgccttatagtgatggttcattaataaagtctaaaaacattttttgaatgcacaatctattgactaaagttggacatgcttctttttcgcagTTTCAGACACCTGGCTTGCGAATCCTGCTTTGCCTGATGATATTCTGAAGGAGGCTGTGCCAGGAAATATTCGGCGAGCAGAGCATTTCTTGTCTGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA