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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttttttttttttctggaaatagatatctttaggaattgggcatctcagatatcttttatttttgaataccacatttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG

Basic information

species Vitis vinifera
transcript Vv10s0042g01220.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 7
tttttttttttttttttctggaaatagatatctttaggaattgggcatctcagatatcttttatttttga-ataccacatttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG
                   | |  || || |   |     |    |   || | | ||  |||| ||| | ||     |  |  || |   ||     ||||| ||| | |  ||||| |||   ||||| ||||| ||||| |||||| | |||||||||||||| ||||| || ||||| ||||| || || ||||| |
-------------------gtatgtatatcttagtcatggtgctaccattctgttctccattatgtttaatatgaacaaaatagcaatggttttgctacagGGAGTTCTTAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTTATGAAAGATGAGAATGGAAACATTAAGTGCACGCCAATCTACTCAAGGATTG

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 7
----tttttttttttttttttctggaaatagatatctttaggaattgggcatctcagatatcttttatttttgaataccacatttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG
     |  ||||          | ||| | | |||  | |    |   |    | | | | |    |  |  || |    ||| ||||| | ||||||| | ||||||||||||| || ||||| || ||||| ||||||||||||||||||||||||||||||| ||| || |||| |||||| || ||||| || || ||||
tgtggtgcttttgcacaaccaattgaatttgttattatgaactttcaagtggtttaaagaccacagacatcagact----catctgacaatttgttctttgaagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGGATTGTTGTTAAAGATGAGAGTGGAAATATCAGATGCACGCCCATATACTCAAGAATAG

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 7
tttttttttttttttttctggaaatagatatctttaggaat-tgggcatctcagatatcttttatttttgaatacca----catttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG
     |  | |||||   |  |||   ||   |||   | | ||  | |   || |            |||  | ||    ||| || || | || |||| ||||||||||||||| || ||||| || ||||| ||||||||||| |||||||||||||| |||| ||| || |||| ||||||||| ||||| || || ||||
-----tggtatttttgcatccaaaccaattgatttgttattatgaactttcaagttgctggaagaccatgagcatcagactcatctgtcaatttgctctttgcagGGTGTTTTGAAGGTCAATCAATTCATTGAAGTTCGTCCTGGCATTGTTGTTAAAGACGAGAGTGGAAATATCAGATGCACACCCATATACTCAAGAATAG

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|110426879|gb|EC993305.1|EC993305
EST:     TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGG                         GGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT
genomic: TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtatct ... ttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT
EST: gi|110702498|gb|EE081278.1|EE081278
EST:     TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGG                         GGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT
genomic: TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtatct ... ttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT
EST: gi|110693290|gb|EE069394.1|EE069394
EST:     TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGG                         GGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT
genomic: TTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtatct ... ttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctcagatatcttttatttttgaataccacatttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG
                                atttgac  putative branch site (score: 4)
                                           tgttctt  putative PPT
      agatatcttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttttttttttttctggaaatagatatctttaggaattgggcatctcagatatcttttatttttgaataccacatttgacattatgttcttggcagGGTGTTTTGAAAGTGAATCAGTTTATTGAGGTTCGTCCTGGGATTGTTGTTAAAGATGAGAATGGGAACATCAAATGCACACCAATATATTCTAGGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - -ggaaata
- - - - - - - - - - - - - - - - - - - - - - -catctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatacca