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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctttgttgttcaaatagtttccttgattggtaaatacctgatctagcatgcaaactattttctgtaaactgttaattatatggttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG

Basic information

species Vitis vinifera
transcript Vv15s0046g02460.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 4
gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctttgttgttcaaatagtttccttgattggtaaatacctgatctagcatgcaaactattttctgtaaactgttaattatatg-gttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG
                   | |    ||||| |  |   |   |  | |||| || |      | |    | | ||| || ||      |||||     ||| |   |    ||  | |  |     | ||  | | |||  | |  ||   ||  |||  | |||  |||||| | || ||||||||||||||| | ||||| || ||||| |  || ||||||||||||||||| ||||| |||||||||||| | | |||||| |||||
-------------------gtaaatcttcaaagccttccac-cacctgaaatcttgtgccatgtcctatgtaggtttttttttt-----gtttcaaattttgttttgtcttggaagttgttttttggccatagtatctaacatatgtatcgaatttgttttcaatttctcagTTTCGGTGCAGCTATACTCTCCAGACCGTCCTCTGGTTGATACTGCAGAGGTGTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctt-tgttgttcaaatagtttccttgattggtaaatacctgatctagcatgcaaactattttctgtaaactgttaa-ttatatggttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG
             ||   ||  ||  ||||  ||| ||      |||     || |   | ||| ||    ||| | ||||  |  ||   ||    |  ||||||| |     ||     |   |   || |    |  | ||   |   ||  |  | |  | ||  |||||    ||  |||| ||||||||| | ||||| || ||||| |  || ||||||||| ||||||| ||||| |||||||||||| | | |||||| |||||
------------gtaaattgtttgtcttca--gttccatgc---tttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 4
gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctttgttgttcaaatagtttcct-tgattggtaaat-acctgatctagcatgcaaactattttctgt-aaactgttaattatatggttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG
||||| ||  | || |      ||  |     |||    || || ||    | |||  |||    ||  |    ||  || || ||||     | | |  ||  || || |  ||| |  |      |  |  | || ||   |||  |   | ||   || | |  |||| |||  |  | ||| |||||||||||  ||||||| | |||||  | || || |||||||||||||| ||||| |||||||||||||||  ||| ||||| ||
gtatgattgactttctatgagctgtctctt--gttgtgtaattaattatggtttttcttttggcacaggacaatttaatttttaaaatgacagcttatattttatatatgatgtgaacatgtgccttacttgatatcggttgcacttctgcgtgtacaatttc-tgctctttagTGTCAATCCAGTTATACTCTCCACTGCGTCCATTGGTTGATGTTGCGGAAGTGTTTTTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 4
gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctttgttgttcaaatagtttccttgattggtaaatacctgatctag-catgcaaactattttctgtaaactgt-taattatatg---gttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG
||||| ||  | || | |    ||  |     |||    || || ||      |||  |||    ||  |  | ||  || || |||||    | |  |||     ||||||||| | | ||||     || ||  | |    ||     ||  |||     | |||  |||| |||  |  | ||| |||||||||||  ||||||| | |||||  | || || |||||| ||||||| ||||| |||||||||||||||  ||| ||||| ||
gtatgattgactttctccgagttgtctctt--gttatgtaattagttacggcttttcttttggcacaggacagtttaatttttaaaataaaggcttatatttt---atacctgatgtggacatgtgtcttacttgatattggttgcacttttgcatgtacaattcctgctctttagTGTCCATCCAGTTATACTCTCCATTGCGTCCATTGGTTGATGTTGCGGAAGTGTTTCTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTG

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|33405906|gb|CF211533.1|CF211533
EST:     ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAG                         TTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
genomic: ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAGgtatgctttc ... tattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
EST: gi|161707763|gb|FC056428.1|FC056428
EST:     ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAG                         TTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
genomic: ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAGgtatgctttc ... tattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
EST: gi|110712809|gb|EE088181.1|EE088181
EST:     CAAGATGCTGGTGCCAGCTTGGGAAAAAAGTTTAA-GAA-AACTCTTCAG                         TTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAACTGAAG
genomic: CAAGATGCTGGTGCCAGCTTGG-AAAAAAGTTTAAAGAACAACTCTTCAGgtatgctttc ... tattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
EST: gi|161714434|gb|FC064433.1|FC064433
EST:     ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAG                         TTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG
genomic: ACAAGATGCTGGTGCCAGCTTGGAAAAAAGTTTAAAGAACAACTCTTCAGgtatgctttc ... tattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcatgcaaactattttctgtaaactgttaattatatggttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG
                          tgttaat  putative branch site (score: 3)
                                        ttccctattcttc  putative PPT
                     taaactgttaattata  TA-rich tract