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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgccaattttcattggttatgctagttacatttaacatttttcactatcagttagtattttcttgttaattttgttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 11
gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgccaattttcattggttatgctagttacatttaacatttttcactatcagttagtattttcttgttaattttgttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG
                                                                      ||  |  ||    |||    | |||  |||  |      |  | |||| || |   |  || ||     || |   | |   | |   || |   ||      |||||  ||  ||  |||||||| |||||||| ||||| || ||||| ||||||||||| ||||| ||| | || | ||||
---------------------------------------------------------------------cagc-atgttacgaattgcaaattattggttttt-caacatgatgaattgtgctttaacatttgaaccacttccttatctggtggcaatttatcacttc-----cagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 11
gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgc-caattttcattggttatgctagttacatttaacatttttcactatcagttagtattttcttgttaat-tttgttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG
                     || | ||  ||||  ||| | |  |   | ||| |    |   | | || |     |  ||   || ||   ||  |||| |||| ||||  | ||| |||    | |  ||     |||||  |||     |  || || | |||||    | |||||| ||||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| || | |||||||
---------------------gtaaaatgaatgccatttgtatgatgcacacaaatgctgt--ataaagccatcagaaactag--ttattacttagtagtt-gtatcttctactaaatgtttagccagacattttttcagttttaact----gaccctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 11
gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgccaattttcattggttatgctagttacatttaacatttttcactatcagttagtattttcttgttaattttgttga-tattttg---gagaagtttacacttttaa---agtcttcttttttttttgg-ttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG
                     || | ||  |||   ||| | |  |   |  |      |||  ||      |||||    |  || ||   ||| |||| |||| ||||    | || |  | | | ||| |   || |  ||| || || |||   |  || || | || ||||   | |||||| |||||||||||||||| |||||||||||||| |||||||| ||||||||||| || ||||| || | |||||||
---------------------gtaaaatgaatgatatttgtatgatgcac--accaatgttgtataaagccattacaaacta-gttattatttattagtt-gtatcttcta--cagttctactaaatgtttagcctgacattttttcagttataactgaccctactgtgttgtttgaactacagAGTTTGTTAGAGAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTAGTGAACTTAAGAAACAAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaaaggctccttgatgctagttacatttatgcagtttttcttgtttgccaattttcattggttatgctagttacatttaa--catttttcactatcagttagtattttcttgttaattttgttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG
                                            ||  |    | ||   || || |  || ||  | || |   |||  |   |||   ||||   | |||||| |  ||||   | | || |    |      ||| | |   |||  | |   || |   |||||| | || | | |||||| |||||  | || ||||| || |||||||| |||||||| ||||||||| |||||||||||
--------------------------------------------gtgcgttg-tgtttgctgattgtcgtatttttacttgagtaattagttgatatgccttaga--tatcttgtcatgtttgg-aacagttggatataagacctactgtaatcatctcatatggcttgtcaatgcagACTTTGCTTGCGAAAGGATATGATTTAGTGTCTGGAGGCACTGATAATCATTTAGTTTTGGTGAATCTGAAAAACAAG

Mapped 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|161709499|gb|FC058863.1|FC058863
EST:     ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAG                         AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGTGGAACTGATAACCAT
genomic: ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAGgtaaaaggct ... ttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
EST: gi|110383662|gb|EC948045.1|EC948045
EST:     ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAG                         AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
genomic: ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAGgtaaaaggct ... ttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
EST: gi|110361032|gb|EC924482.1|EC924482
EST:     ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAG                         AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
genomic: ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAGgtaaaaggct ... ttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
EST: gi|351022221|gb|FQ438806.1|FQ438806
EST:     ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAG                         AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
genomic: ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAGgtaaaaggct ... ttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
EST: gi|351043008|gb|FQ434449.1|FQ434449
EST:     ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAG                         AGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT
genomic: ACAAGGCTTATCAAGAGCAAGTCCTTACTAATTGCTCAACATTTGCTCAGgtaaaaggct ... ttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatattttggagaagtttacacttttaaagtcttcttttttttttggttgcagAGTCTGTTAGAGAAAGGCTATGAACTTGTATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG
 tgttgat  putative branch site (score: 4)
                                tcttcttttttttttg  putative PPT
                        ttttaaagtcttcttt  TA-rich tract