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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaacatgtgaaaacaaaagtatgtatgcctctttacagttttcttagattgggaactcaacttgtttgtcttgtttcctccgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGATGGGTTATG

Basic information

species Vitis vinifera
transcript Vv05s0020g03200.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G28340.1 (Glycine max), 3'ss of exon 7
gtaagtaacat----gtgaaaacaaaagtatgtatgcctctttacagttttcttagattgggaactcaacttgtttg---------------------tcttgtttcctccgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGATGGGTTATG
||||||  | |    | ||||| |||||  | | |    || |  ||||||    | ||    |   |  |  ||||                      ||| ||| ||    | ||||||||||||| |||||||||| || || || |||| |||||||||||||||||||||||||
gtaagtgtcttccgagggaaaagaaaagattattttttcctattaagtttttcctggttcaatataaagttcttttgacatcaattgcatcaaattccccttcttttcttttgtttgcagATGTTGTGCCTTATTCAGCTCACATCCCATCCTATGCTGATATTTGGGGATGGGTTATG

upper sequence: Vv05s0020g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G39440.1 (Glycine max), 3'ss of exon 7
gtaagtaacatgtgaaaacaaaagtatgtatgcctcttt-----aca-gttttcttagattgggaactcaacttgtttg---------tcttgtttcctccgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGATGGGTTATG
||||||    |    |   ||||| | ||||  || |||     | | |||||    | ||    |     ||  ||||         ||   ||| ||    | ||||||||||||| |||||||||| || || || |||| ||||||||||||||||||||| |||
gtaagtggtcttcccagggaaaagaaagtattactttttttctaatatgtttttcctggttcaatataatgctcttttgacatcaaattcaccttttcttttgtttgcagATGTTGTGCCTTATTCAGCTCACATCCCATCCTATGCTGATATTTGGGGATGGGTCATG
















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|352791045|gb|FQ480038.1|FQ480038
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGAAATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
EST: gi|351055343|gb|FQ441941.1|FQ441941
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCATCCCATATTCCTTCCTTTGCTGATATTTGGGGAA
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGA-
EST: gi|349822939|gb|FQ399918.1|FQ399918
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCCTCAAAC                         ATGTTGTGGCTTATTCA
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCA
EST: gi|351039310|gb|FQ461177.1|FQ461177
EST:     ACAGAGGTTTTCTCTTGCATTCACAACACCCCTAAG-CAGGTCTTCAAAC                         ATGGTGTGGCTTATTC
genomic: ACAGAGGTTTTCTCTTGCATTCACAACACCC-TAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTC
EST: gi|351049434|gb|FQ450035.1|FQ450035
EST:     ACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTTCAA-C                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGA
genomic: ACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTT-CAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGA
EST: gi|351038474|gb|FQ464340.1|FQ464340
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTAATCAGCCC
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCC
EST: gi|349824845|gb|FQ414703.1|FQ414703
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATT
EST: gi|351049225|gb|FQ449947.1|FQ449947
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATAT
EST: gi|351048095|gb|FQ441267.1|FQ441267
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
EST: gi|351048233|gb|FQ442203.1|FQ442203
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTTGCTGATATTTGGGGA
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTT-GCTGATATTTGGGGA
EST: gi|351052302|gb|FQ455474.1|FQ455474
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
EST: gi|351022726|gb|FQ428635.1|FQ428635
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
EST: gi|349815985|gb|FQ403626.1|FQ403626
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCATCCCATATTCCTTCTTTTGCTGATATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
EST: gi|351039295|gb|FQ461162.1|FQ461162
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATA
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATA
EST: gi|351047673|gb|FQ455070.1|FQ455070
EST:     TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAAGCAGGTCTTCAAAC                         ATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT
genomic: TACAGAGGTTTTCTCTTGCATTCACAACACCCTAAGGCAGGTCTTCAAACgtaagtaaca ... cgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttttcttagattgggaactcaacttgtttgtcttgtttcctccgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGATGGGTTATG
                         cttgtttgtcttgttt  CT-rich tract
        ttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaacatgtgaaaacaaaagtatgtatgcctctttacagttttcttagattgggaactcaacttgtttgtcttgtttcctccgttgtgcagATGTTGTGGCTTATTCAGCCCATATTCCTTCCTTTGCTGATATTTGGGGATGGGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT