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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttttctgattttctcgtttttttagatgagaattgtgctattgatgaaagggaatattttggggtttctttgttttttattttttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTTGCGCCAATGCCGCAGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g01770.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G829928_T02 (Zea mays), 3'ss of exon 1
-gttagtttttctgatttt-ctcgtttttttagatgagaattgtgctattgatgaaagggaatattttggggtttctttgttttttattttttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTTGCGCCAATGCCGCAGAAG
 | | |   | ||        |       | | |||   || ||  | |   | ||  |        |    || ||  |      |||| |  |    |||||||||| || || |||||||| ||  | ||| ||||||| ||||||||||| || ||||||||||||
tgctggcgatgctacccagattaacaacatcacatgtacat-gtcttctgactcaattgtgtggcgctcatcttgctgagcacggcatttctgcgcaacagATGTATGTCACGCCACCGGACACCGACATCTACTCCATTCCGAGGGTTCTTGCCCCGATGCCGCAGAAG

upper sequence: Vv18s0001g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G09200.1 (Glycine max), 3'ss of exon 1
gttagtttttctgattttctcgtttttttagatgagaattg--tgctattgatgaaagggaatattttggggtttctttgttttttattttttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTTGCGCCAATGCCGCAGAAG
|||  |    || ||  |  |    ||  |    |    |   |  | ||          ||  |||    |||   || |   |  || || | | |||||||||||||||||||||||| || ||||| ||  | ||||| | |||||| || |||||||||||||||
gtttctaaccctaataataccacgcttcgaatccatgcatacctcttcttttctttgttcaacttttcaccgttgagttttgaatctttgttcgttcgtagATGTATGTTACTCCTCCGGATACAGATGTTTATTCAATTCCCAAGGTTCTCGCTCCAATGCCGCAGAAG

upper sequence: Vv18s0001g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G12370.1 (Glycine max), 3'ss of exon 1
gttagtttttctgattttctcgtttttttagatgagaattgtgctattgatgaaagggaatattttggggtttctttgttttttattttttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTTGCGCCAATGCCGCAGAAG
|||      |  |||| |  |  || ||    |     || || | ||| | ||        |||    |||   |||      | | |||| | ||||||||||||||||||||| || || ||||| ||  |  |||| | |||||| || |||||||||||||||
gttctacacttcgattctacctcttcttcttctt----ttttgttgttgttcaa------cttttcaccgttgagttg------aatctttgttcgtagATGTATGTTACTCCTCCAGATACAGATGTTTATTCAGTTCCCAAGGTTCTCGCTCCAATGCCGCAGAAG

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|349826810|gb|FQ418901.1|FQ418901
EST:     TCATTAGGAAGCCGCCTGATCCGGATAACGATGTCTACGACTTCAGAGAG                         ATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTT
genomic: TCATTAGGAAGCCGCCTGATCCGGATAACGATGTCTACGACTTCAGAGAGgttagttttt ... ttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTT
EST: gi|349824926|gb|FQ406465.1|FQ406465
EST:     TCATTAGGAAGCCGCCTGATCCGGATAACGATGTCTACGACTTCAGAGAG                         ATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTT
genomic: TCATTAGGAAGCCGCCTGATCCGGATAACGATGTCTACGACTTCAGAGAGgttagttttt ... ttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatgaaagggaatattttggggtttctttgttttttattttttggttgtagATGTATGTTACTCCTCCGGACACTGATGTGTACGCCATTCCAAGGGTTCTTGCGCCAATGCCGCAGAAG
 tattgat  putative branch site (score: 3)
                          tttctttgttttttat  putative PPT
                          tttctttgttttttat  TA-rich tract