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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgctctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG

Basic information

species Vitis vinifera
transcript Vv03s0038g02380.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 3
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgctctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
 | |  |||     |  | |||    |||| |  ||   ||| |  |  |      | ||  ||  |   ||    ||| ||||        | |   || ||||   || |||||||||| |||||| ||| |||||||||||| ||||| || || || ||||| || ||||||||||
-ttatgttgatacttgatttgatcatttttgtggctcgattcactttttta----gtctccacttat-ggtacttcttgttgat--------tctaaactttgttat-at-ttcagTGGATACCTGAGCTGAAGCATTATGCACCTGGTGTGCCTATCATCCTTGTGGGAACAAAGCTTG

upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 3
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgctctg-----tttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
                  |   || | |  | |||    | |    |  || |     |       |  | |||| || |  |    || |||     |||||      ||  || |||||||||| |||||  ||| |||||||||||| ||||| ||||||||||| || |||||||||||||
------------------agtggaaactgatgtccaaaat-caaatttttgaataggattaatccat--agatggcttccaaacttcttgtttgctgactctgaaccccttttattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG

upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgct---------ctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
                          | |  |       ||||||    | ||   |    |  | ||||||| | | |||   ||| | ||| | ||||         |   ||| || |||||||||| |||||  ||| |||||||||||| ||||| ||||| ||||| || |||||||||||||
-------------------------gtgtactgaaacagttctccaaaatccatttttgaataggattaatatagatggctcccaaactttttgtttgctgactctgaaccccttctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG

upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 3
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgctctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
                        |     ||  | |||||||   || |      ||||  ||   || | |||  |       |||| |||       | ||   ||| ||||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| ||||
------------------------gtaagcttggcatttttctttttcttttgttttgtc-cctctctactctggact-------aatttttt------cccgt---cattttcagTGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG

upper sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 3
gtaagtttggcttctactatgagagatttttttccttttttctccctcctgcaacatgtcgtctggttaatatggtttgctgataaattctttatgtgctctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
                 || |   |  |||||| ||||||| |   |  || |         ||   |||| |||  |       |||| | |            ||| | | ||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| ||||
----------------gtaagcttgggttttttactttttttttttttttgta--------cctctctaatctggact-------aattttctcc--------catccttgtccagTGGATTCCTGAGTTGAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG

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|27581311|gb|CB004006.1|CB004006
EST:     TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAA                         TGGATTCCTGAGTTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTC
genomic: TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAAgtaagtttgg ... ccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTC
EST: gi|77585106|gb|DV221640.1|DV221640
EST:     TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAA                         TGGATTCCTGAGTTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTC
genomic: TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAAgtaagtttgg ... ccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTC
EST: gi|161720989|gb|FC070698.1|FC070698
EST:     TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAA                         TGGATTCCTGAGTTGAGGCATTATGCACCTGGTGTTCCAATAATTCTTGTC
genomic: TTGCTTTCTCCCTCATTAGCAAGGCTAGCTATGAAAATGTTGCCAAGAAAgtaagtttgg ... ccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggttaatatggtttgctgataaattctttatgtgctctgtttccatattcagTGGATTCCTGAGTTGAGGCATTATGCACCCGGTGTTCCAATAATTCTTGTCGGGACAAAGCTTG
                tgctgat  putative branch site (score: 3)
                                     ctctgtttcc  putative PPT
                   tgataaattctttat  TA-rich tract