Sequence
atgc intronic sequence ATGC exonic sequencegtttggatcactttatgtttttctttttctttttttattgattttttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 2
gtttggatcactttatgtttttctttttctttttttattgattttttgaattgtaatgatttaatattgtttaattgctgtgatgatt--tactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
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aaatatacta-ttggtgtgatcacattcaatgcctggttt-tatttagaggaaacacaggttatttttctgtgagaactgaaccctctgattcttacaacagGCTGCTCAACCATTCTTCTTGTTAGCTGGGCCTAATGTGATTGAATCAGAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAA
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 2
gtttggatcactttatgtttttctttttctttttttattgattttttgaattgta-atgatttaatat-tgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
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agtttcttcgtttgccctcacatgaatgatataaacgacaacttttgtgatcatgtattatgtactgtgtgtttttttatcaatctgatt--cttgcaacagGCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 2
-------------------------gtttggatcactttatgtttttctttttcttttttt--attgattttttgaattgtaatgatttaatattgtttaattgct-gtgatgattt-actgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
|||| | ||||| ||||||| || | | ||| || ||| || | | ||| ||| | | || | | ||| | ||| | | | ||| |||| || || ||| || | || ||||| |||||||||||||| |||||||||||| || ||||| || |||||||| | | |||| |
gtccgtcatttctcgctgattatgagtttctag-actttgaatttttctgggtcatgacctgaattccttctttttcttatttttttttttaattttctgatgggtcgtgtttctttcaatctcaccagGGTGCAGACCCGTTCTTCCTGCTAGCGGGTCCTAATGTGATTGAATCAGAGGAGCACATTCTGCGGATGGCTAAGAACATCAAGACTATTGCATCTGA
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 1
-----------------------gtttggatcactttatgtttttctttttcttttt-----ttattgattttttgaattgtaatgat-ttaatattgtttaattg-ctgtgatgattt-actgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA-
||| ||||| ||||||| || || | |||| | | || | | | | ||| || | | || | |||| | ||| | | | ||| |||| || || ||| || | || ||||| |||||||||||||| |||||||||||| || ||||| || |||||||||| | |||| |
tccgtgatttctcgctgattattattttctagactttgaatttttctgggtcaaggccaaaattctcttttttcttattttttttattctcaattttctctgatgggttgtgtttctttcaatctcaccaggGTGCAGACCCGTTCTTCCTGCTAGCGGGTCCTAATGTGATTGAATCGGAGGAGCACATTCTGCGGATGGCTAAGAACATCAAGAGTGTTGCATCTGAG
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G79500.5 (Arabidopsis thaliana), 3'ss of exon 1
gtttggatca--ctttatgtttttctttttctttttt----tattgattttttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
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---cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgtt-ggcttcttacggtaaaatcgagtttgatt-ctaatacg-tatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G79500.2 (Arabidopsis thaliana), 3'ss of exon 2
gtttggatcactttatgtttttctttttctttttttattgat--tttttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
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---------gtttgagtctcgcctttttgttttcagaatgttgaatgttggcttcttacggtaaaatcgagtttgatt-ctaatacg-tatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|110708160|gb|EE085385.1|EE085385EST: GTGTGTAAAAAACCATGGATTCTTCAACAATGCTGTACAACCAGCTCAAG TCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAG
genomic: GTGTGTAAAAAACCATGGATTCTTCAACAATGCTGTACAACCAGCTCAAGgtttggatca ... ctgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAG
EST:
gi|30252416|gb|CB969967.1|CB969967EST: GTGTGTAAAAAACCATGGATTCTTCAACAATGCTGTACAACCAGCTCAAG TCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAG
genomic: GTGTGTAAAAAACCATGGATTCTTCAACAATGCTGTACAACCAGCTCAAGgtttggatca ... ctgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
gtttaat putative branch site (score: 4)
ttgtaatgatttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggatcactttatgtttttctttttctttttttattgattttttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA