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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaagcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG

Basic information

species Vitis vinifera
transcript Vv08s0007g03250.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggt-gcgtccaaacaggtgctaagcttcaaaattt----tgtttctaag-tgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
    | ||     || |      ||||| |     |||  | |    |||  || | ||  || ||| |  |     |||  || |    |  |  || | |||||||||||||||||||||| ||||| ||||||||||| |||| ||| || || ||  |||  |  |||||||
----tttcccttcacttaggatatttgggt--gttctttctgtctggaagaagtagtgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G022866_T01 (Zea mays), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG------------------------------
||    ||| |      | |     |  |||      |   ||||| |   | |   ||  |    ||| |||  | | || ||  |        | |||||||||||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||                              
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatc--attcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGGTGTGTATTCAACACATCTCCTTTTCACTT

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
||    ||| |      | |     |  |||      |   ||||| |   | |   ||  |    ||| |||  | | || ||  |        | |||||||||||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatc--attcagtgttaacagttacataagatgcacctctattgcagGTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G825090_T03 (Zea mays), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
||    ||| |      | |     |  |||      |   ||||| |   | |   ||  |    ||| |||  | | || ||  |        | ||||||| |||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatc--attcagtgttaacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G085000_T03 (Zea mays), 3'ss of exon 4
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
 |  | || |   | ||    ||   | | ||||     | ||| |           | | |    ||| |||  | |  | ||  |   |    | ||||||||||||||||||| || || || ||||||||||| |||||||| || || ||  | | ||  | |||||
cgggtgtcatctgagattt--cccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G825090_T05 (Zea mays), 3'ss of exon 5
tgcatctcttaaaacatc--aagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgcta-agcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
    |||  | |    ||  |||   |   |||      |   ||||| ||   || |   ||  ||| |   | || | || ||  |        | ||||||| |||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||
--ggtcttctgagttttcccaagaaataaaattgcgtaatgaaatgca-aatcagttctatcattcagttataacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G804772_T03 (Zea mays), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG------------------------------
||    ||| |      | |     |  |||      |   ||||| |   | |   ||  |    ||| |||  | | || ||  |        | ||||||| |||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | |||||                              
tggtcatctgagttttcccaagaaataaattgcgtaatgaaatgcaaatcagttctatc--attcagtgttaacagttacataagatgcacctctattgcagGTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGGTGTGTATTCAACACATCTCCTTTTCACTT

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA0084S00210.1 (Glycine max), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaagcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
|| |||| | |   | |      | | | || | | | ||||   |       || ||   | | |      | | |    ||||  ||  |   | ||||| || ||||||||||| | | ||||||||||||| ||||||||||||  |||||||||||  |||||||
tgtatctatcatcgctttccttatcttgcttcatgatgattacatagtgcttttgagtgagacctgagaaatatcgtttttatttgtttattggtttcagGTTGACCCAAACACAGGCGCTTCAATGTATGAATCAGATGACATAATTCGGTATTTGGTTGACAAATATG

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G22160.1 (Glycine max), 3'ss of exon 5
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaagcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
||        |  || |      | | | || | | | ||||   |       || ||   ||| |      | | |     |||| ||  |   | ||||| || ||||||||||| | | ||||||||||||| ||||||||||||  |||||||||||  |||||||
tgttatctacatcactttccttatcttgcttcatgatgattacatagtgtttttgagtgagaactgagaaataacatttttctttttttattggtttcagGTTGACCCAAACACAGGCGCTTCAATGTATGAATCAGATGACATAATTCGGTATTTGGTTGACAAATATG

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|30253288|gb|CB970839.1|CB970839
EST:     TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|349822639|gb|FQ412903.1|FQ412903
EST:     TCCGTCCCAAGGTTTCTCATATGGGTGGAAAACAGCACTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|27755146|gb|CB035901.1|CB035901
EST:     ATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: ATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|30253209|gb|CB970760.1|CB970760
EST:     TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|351019188|gb|FQ429348.1|FQ429348
EST:     TCCGTCCCAAGGTTTCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|110413628|gb|EC979423.1|EC979423
EST:     TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTTCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCAGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|110423056|gb|EC989391.1|EC989391
EST:     TCCGTCCCAAGGTTTCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|28959489|gb|CB339745.1|CB339745
EST:     TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAGACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
EST: gi|349811972|gb|FQ410769.1|FQ410769
EST:     TCCGTCCCAAGGTTTCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATG                         GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG
genomic: TCCGTCCCAAGGTTGCTCAGATGGGTGGAAAACAGCAGTTCCCTTACATGgtttgataac ... ctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaggggtgcgtccaaacaggtgctaagcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
                                     ttttgtttct  CT-rich tract
                                 aaaattttgtttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaagcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG

- catctct
- - - - -taaaaca
- - - - - - - - tcaagcc
- - - - - - - - - - - - - - - - - - - - tatgcac
- - - - - - - - - - - - - - - - - - - - - - - - aggggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcaaaa