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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctctggtgaaaatttgattgaaactaagatttgttgcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA

Basic information

species Vitis vinifera
transcript Vv11s0065g00480.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g26440.1 (Oryza sativa), 3'ss of exon 5
ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctct-ggtgaaaatttgattgaaactaagatttgttgcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA
      |  | ||| | |||   |  |      |||    |  |  | | | |||| |  ||      | |    ||| |  | |    ||  |    |||||||||||||||||  | ||||||||| ||||||| || ||||||||| | || ||||| || ||||| || || || || || || || ||| | || |
-----gtatgcttgaacctctagatatgtttcttacctttaacatgtcgaaactctagaagagggagagttcctgacttatttattactcatatgaaccagACTTCCAAGGAATATCTTGAGAAGCAGTTGGCAGAAGTGGAGAACAACATAAGAGAGCTACTTCAGCAGGACCCTGGGCTGGCACGCCAGATCCTATCAA

upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G26710.1 (Glycine max), 3'ss of exon 5
ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctctggtgaaaatttgattgaaactaagat-ttgttgcacg---ttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA
        | | |   | ||  |    |   |||| | |   |||  ||  | ||   | |   |||||  |||| |||| | || ||  | |   ||| |||||  || || |||||||| || || |||||||||||||| || | |||  |||| || ||||| || |||||||| ||||||||| | ||||||||||| |
---aaacaaatataactatcttagctaaatttctaaagcagtaaatatgactttcca-taatcttttgagcgaaaataagttcttattatatggctttgaacagAGCTCAAAAGAATACTTGGAAAAACAGATGGCAGAGGTGGAAACCAATTTGAGAGAACTGCTACAACAAGATCCTGGTCTTGCTAGGCAAATCATGTCTA

upper sequence: Vv11s0065g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G07340.1 (Arabidopsis thaliana), 3'ss of exon 5
ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctctggtgaaaatttgattga-aactaagatttgtt----gcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA
      | |   |   || | |   | |||   ||       |   ||          ||| |   || ||   ||  | | ||||||    | | | |    |||| |||||||||||||| ||||||||| | |||||||| ||||||||| ||||||||||| |||||||||| || ||  ||||||  || || ||||| |
-----gtaacaatcattccctctttcaacatcttattgggtta---ttaggagatcattgagatgctggttatcaaacatgttttgttttcgggatgatttttagACATCCAAGGAATACTTGGAGAAGCAGGTAGCAGAGGTTGAGAACAACTTGAGGGAGCTGTTGCAGCAAGAACCGGGCATTGCTCAACAGATTATGTCCA

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|110396623|gb|EC962315.1|EC962315
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|351043316|gb|FQ451368.1|FQ451368
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCCGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|71873337|gb|DT022392.1|DT022392
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|351016504|gb|FQ423931.1|FQ423931
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110380311|gb|EC945566.1|EC945566
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110421110|gb|EC987398.1|EC987398
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110390962|gb|EC955912.1|EC955912
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCCGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110428276|gb|EC994743.1|EC994743
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110392562|gb|EC958071.1|EC958071
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|30138026|gb|CB923364.1|CB923364
EST:     GAAGCCGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: GAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|351022560|gb|FQ447082.1|FQ447082
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
EST: gi|110414808|gb|EC980666.1|EC980666
EST:     AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAG                         ACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG
genomic: AACAGGAACAGAAGCTCAAGGATAGTGAAGCTGCAATTGCTGGTTTACAGgtctgctttt ... cgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtatctctggtgaaaatttgattgaaactaagatttgttgcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA
                  atttgat  putative branch site (score: 5)
               aaaatttgattgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggcttgagtttggatctcacaagctacagtctacaaccacaaacttgtatctctggtgaaaatttgattgaaactaagatttgttgcacgttggacagACTTCCAAGGAATACTTAGAGAAGCAGATGGCAGAGGTAGAGAACAACCTGAGGGAGCTGCTGCAGCAAGATCCAGGTCTTGCTCGTCAAATCATGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
-gggcttg
- - - - - - - - - -cacaagc
- - - - - - - - - - - - - - - - - acaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca