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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatccctttgtttcttttaaacttaaaagtatttagccttgtgtttgtagtttaccatacatggactcttgatattatatttctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAGAAAAGGTTATTTTGACAGTGAAGCCACAAT

Basic information

species Vitis vinifera
transcript Vv00s0769g00010.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G10730.1 (Glycine max), 3'ss of exon 4
gttagtatccctttgtttcttttaaacttaaaagtatttagccttgtgtttgtagt-ttaccatacatggactcttgatattatatttctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAGAAAAGGTTATTTTGACAGTGAAGCCACAAT
|| |||  ||   || || | ||   ||    | |||| ||  || | ||| | || | | |  ||||  |   ||   | | ||||       |||| | |||| ||||||||  | ||||||||||| || || |||||||| ||||| || ||  |||||||||||||||||||||
gtcagtg-cctactgattttgttgctctcttta-tatt-agttttttttttattgtgtgatctaacattaatgttt---actgtatt-------acagGTCATTTTTGTCCTGCTTTTTCCAAGGCTGTTAAAACCATGAAGAAGGGAGAGAAAGTGCTTTTGACAGTGAAGCCACAAT

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 4
gttagtatccctttgtttc-ttttaaacttaaaagtatttagccttgtgtttgtagtttaccatacatggactcttgatattatatttctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAGAAAAGGTTATTTTGACAGTGAAGCCACAAT
|| | |  |   |  |||  ||     ||| | | || ||  | ||   | |||  | |    |||||  |   ||   | | ||||       |||| |||||| ||||||||  |||| |||||||| || || |||||||| ||||| || ||  || ||||||||||||||||||
gtcactgcctactaattttgttgctctcttcatattaattttcttttattgtgtgatct----tacattaatgttt---actgtatt-------acagGTTATTTTTGTCCTGCTTTGTCAAAGGCTGTTAAAACCATGAAGAAGGGAGAGAAAGTGCTTCTGACAGTGAAGCCACAAT
















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|110689824|gb|EE066384.1|EE066384
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|71873918|gb|DT022973.1|DT022973
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATG
EST: gi|34546871|gb|CF515103.1|CF515103
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|30132799|gb|CB918138.1|CB918138
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|30132743|gb|CB918082.1|CB918082
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|110699844|gb|EE077215.1|EE077215
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|110365463|gb|EC928491.1|EC928491
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|34546797|gb|CF515029.1|CF515029
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|34548843|gb|CF517075.1|CF517075
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|29783511|gb|CB349715.2|CB349715
EST:     TGGCACCTTGTTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|110700523|gb|EE078663.1|EE078663
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAAGCTGTGAAGACAATGAAGAAA
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAA
EST: gi|110690423|gb|EE067508.1|EE067508
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|34550935|gb|CF519143.1|CF519143
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATG
EST: gi|110699434|gb|EE076427.1|EE076427
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|352769557|gb|FQ468485.1|FQ468485
EST:     TGGCACCTTGGGTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCCAAG-CTGTGAAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCC-AAGGCTGTGAAG
EST: gi|28969463|gb|CB348496.1|CB348496
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAACGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|34546618|gb|CF514850.1|CF514850
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTTGAGTTCACTGTCAAAGAGG                         ATTATTTTTGTCCTGCCCTGGCCAAGGCTGTGAAGACAATGAAGAAAGGAG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAG
EST: gi|34550055|gb|CF518287.1|CF518287
EST:     TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGG                         ATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATG
genomic: TGGCACCTTGGTTGCAAAATCTGATGGTGTAGAGTTCACTGTCAAAGAGGgttagtatcc ... ctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgtttgtagtttaccatacatggactcttgatattatatttctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAGAAAAGGTTATTTTGACAGTGAAGCCACAAT
                             tcttgat  putative branch site (score: 4)
                                        tatttct  putative PPT
                             tcttgatattatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatccctttgtttcttttaaacttaaaagtatttagccttgtgtttgtagtttaccatacatggactcttgatattatatttctgtgaacagATTATTTCTGTCCTGCCCTGTCCAAGGCTGTGAAGACAATGAAGAAAGGAGAAAAGGTTATTTTGACAGTGAAGCCACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC