Sequence
atgc intronic sequence ATGC exonic sequence...agaaacatttttaattgtttttattaagaatgaactttgttcaaatacgggcccatcctatttcttttctttttctaacttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 2
agaaacatttttaattgtttttattaagaatgaactttgttcaaatacgggcccatcctatttcttttctttttctaacttgtcat--cattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
|| | ||| || | | ||| ||| || |||| | | ||||| || | | | |||| | || | ||| |||||| | |||| | ||||||||||||||||| ||||| || ||||| ||||| |||| |||||||| || ||||| || | | ||| ||||||
ttcaatgcatcacatttttgtgtatgtcaattaacatt--tcaataatttaataacactattgacttccaatactgtatttgtgctggtatggaatacacagATTTGATATACTGGGACTTCATGAGTTTGATAGTGATCGTAAGAGAATGTCTGTTATCGTGGGCTGCCCTGATAAGACTGTTAAGCTGTATGTGAAAGGT
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 4
----------------agaaacatttttaattgtttttattaagaatgaactttgttc--aaatacgggcccatcctatttcttttctttttctaacttgtcatc-----attggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
| ||| | | || || | | | || || | ||| | | || | || | | ||||||||| ||||| || ||| |||||||| |||| |||||| ||||||| ||||| |||||| | || || ||||||||||||||||||| ||||||||| | |||||||||||||| |||||
gtgatttctcctgctaacaaaaactaacaa--attaacaattaacatttttttcatcaagaaaaaaaaaacaatggtgattactctttttttctaatgaatcatcccattatgagcattgcagGTTCAATGTCTTGGGTATGCATGAATTTGACAGTGACAGGAAGAGAATGTCAGTTATATTGGGGTACCCTGACAATTCAGTGAAAGTTTTTGTCAAAGGA
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 3
agaaacatttttaattgtttttattaagaatgaactttgttcaaatacgggcccatcctatttcttttctttttctaa-----cttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT---------------------------------
| | | | | || | || | | ||||||||| | | ||| || ||| |||||||| |||| |||||| ||||||| ||||| |||||| | || || ||||||||||||||||||| ||||||||| | |||||||||||||| |||||
--------------------------------------atcaagaaaaaaaacaatggtgattactctttttttctaatgaatcatcccattatgagcattgcaggttcaatgtcttgggtatgcatgaatttgacagTGACAGGAAGAGAATGTCAGTTATATTGGGGTACCCTGACAATTCAGTGAAAGTTTTTGTCAAAGGAGCAGACACATCCATGCTTAATGTGATAGACAGG
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 4
agaaacatttttaattgtttttattaagaatgaact-ttgttcaaatacgggcccatcctatttcttttctttttctaac-----ttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
| || | ||| | |||| | | || ||| | | || || | | || || ||| || || || ||| |||||||| |||| || ||||||||||| |||||||||||||| ||||||||||| |||||||| |||| | | |||| |||||||| ||||||| |||||
------gtgatttagtgtgctatgtaagtttatgcaatttttcctgtgtaatgacgtcacatggttatcctcattttaatgaatatttctattatgggcgatgcagGTTCAATGTCTTAGGTTTGCATGAATTTGATAGTGACCGAAAAAGGATGTCGGTTATATTAGGGTACAATAACAATTCTGTGAAACTTTTTGTTAAAGGG
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G24580.1 (Glycine max), 3'ss of exon 3
agaaacatttttaattgtttttattaagaatgaactttgt-tcaaatacgggcccatcctatttcttttctttttctaacttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
| || | | | | | || | || | | ||| || | ||| | | || || || | | || || || || |||||||| |||| || ||||||||||| ||||||||||| || ||||||||| |||||||||| |||| | | |||| |||||||| ||||||| |||||
-gtaatttactatgctatgtaagtttatgcaatttttcctgtgtaatgaggtcacatagttatcctctttttaatgaatatttctattatgggggatgcagGTTCAATGTCTTAGGTTTGCATGAATTTGATAGTGATCGAAAAAGGATGACAGTTATATTAGGGTACAGTAACAATTCTGTGAAACTTTTTGTTAAAGGG
upper sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 2
-------agaaac---atttttaattgtttttattaagaatgaactttgttcaaatacgggcccatcctatttcttttctttttctaacttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
||| | || || || || | ||||| | | | | | || | | | | || | || | | | | |||||||| ||| |||||||||| ||||||||||| ||||||||||| ||||| |||||||| ||| |||| ||||| |||| | |||||| | ||||||||||||
gtaatttagacatgtgatggctactttttgtcattaattttatattgtcattgcatctcatagtagattgtggccattagtatttattccttttcctttgcccagtgcagATTTAATGTTTTGGGATTGCATGAGTTCGATAGTGACCGAAAAAGAATGTCAGTGATACTGGGATGCCCCGACATGTCGGTGAAACTCTTTGTAAAAGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgggcccatcctatttcttttctttttctaacttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
ttctaac putative branch site (score: 1)
tatttcttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaacatttttaattgtttttattaagaatgaactttgttcaaatacgggcccatcctatttcttttctttttctaacttgtcatcattggcagtgcagGTTTGATGTTTTGGGTTTGCATGAGTTTGATAGTGACCGTAAAAGGATGTCAGTTATATTGGGGTGCCCTGACAACACTGTGAAAGTTTTTGTAAAAGGT
-gaaacat
- - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - -caaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcatca
