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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataagagtcaaagcacaaaatcagcaccttactgctgtatgacatttgtttatcaatatattttacctgacaattttattattaattttctacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG

Basic information

species Vitis vinifera
transcript Vv01s0010g01740.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 10
ataagagtcaaagcacaaaa--tcagcaccttactgctgtatgacatttgtt-tatcaatatattttacctgacaattttatta-ttaattttctacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG
    || |  | | | ||||  |  | | ||       |   |  ||   || | |    |  | |  |     |||    | | ||||   | || ||  ||||||||| |||||||||||||| |||| ||| | ||||||||| || | || ||||| || |||||  | |||||||||
----gaatggaggtataaaagatatgtatctaggaagagaggggtatcaattatgtttgcaggtatgtcaaaggaatccgctgacttaagcatgtatattgcagATGTGCCTTAATGCGTTTGATAAAGCAGCAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------ataagagtcaaagcacaaaatcagcaccttactg-ctgtatgacatttgtttatcaatat-----attttacctgac-aattttattat-taattttctac--atgac--agATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG
                 |||  | | | | ||  | | ||  | |||  ||  || ||    | ||||  |  || |     |    | || || |  | | | || | || ||||    |||    ||||||||||| ||||||||||  | || ||| | |||||||| || ||||| ||||| |||||||| ||||||||| ||
gtaaagatatacacatcatactattgataccattagacca-tatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------------ataagagtcaaagcaca-----------aaatcagcacct-tactgctgtatgacatttgtttatcaatatattttacctgacaattttattattaattttctacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG
                                |||    ||||  |  |             || | |  || |||  | |  |    |  ||||   |||  | | || |  |   |||| | ||| | | | |   |   |||||||||||  ||| || ||| | |  |||||||||||||| || |||||||| || || ||||| ||||||||||||
gtaaagacacacatgaacaaatctttatgttgatatctatcaatccttaccttcttggttggattatcttctctacaacaggctatagtcagttttggaattaaatctaaccaaagcttttgtcatttaatatttgttt---agATGTGCTTTGCTGCTTTCGATGAGGGGGCAAACCTTGATGTGTTAGATCACCCCATCCTTAACTTCATATATTACCTG

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|30137883|gb|CB923221.1|CB923221
EST:     GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATG                         ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC
genomic: GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATGgtgagtcctc ... tacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC
EST: gi|22013779|gb|BQ798813.1|BQ798813
EST:     GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATG                         ATGTGCTTTAATGCGTTTGATAAAGCTGCAAACCTTGATGTTTTGGATCAC
genomic: GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATGgtgagtcctc ... tacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC
EST: gi|110411137|gb|EC976839.1|EC976839
EST:     GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATG                         ATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC
genomic: GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATGgtgagtcctc ... tacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC
EST: gi|30136439|gb|CB921777.1|CB921777
EST:     GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATG                         ATGTGCTTTAATGCGTTTGATAAAGCTGCAAACCTTGATGTTTTGGATCAC
genomic: GCTACGTCACCACCATATGTTTCTCATGTTTCCTTGTTAGATGCATTATGgtgagtcctc ... tacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttatcaatatattttacctgacaattttattattaattttctacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG
                                  tattaat  putative branch site (score: 2)
                                        ttttctac  CT-rich tract
     tatcaatatattttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataagagtcaaagcacaaaatcagcaccttactgctgtatgacatttgtttatcaatatattttacctgacaattttattattaattttctacatgacagATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTG

ataagag
- - - - caaagca
- - - - - - - - - - -cagcacc
- - - - - - - - - - - - - - - actgctg