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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA

Basic information

species Vitis vinifera
transcript Vv07s0031g01970.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 4
gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaaacactaaccccgttgt-ttgtttttatat-tacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
        ||  |  || | |  |    |  |        ||   |   |  |  | | || | || |||| ||   || ||||  |      ||  | |      | |  | ||||| |||||||||||  | |||||||| || ||||| |||||||||||||| || || 
------gtaagttcaagctgcactataatcatggcacacagttacatctactataaccaccatagtgttgtcttcgcatctacataa------tgtctaacaa-gttcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 4
gtcagttaaaaat--agagttaccatgggcttttt-----atttttggtattag-aaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
||||||   || |  | |  |   ||||  ||| |     |  |||||| || | |   |||||          ||   | | | ||  ||   ||   || ||||| || |||||   ||||||||||| |||||||| ||||| |||||||| ||||| ||||||||||||||||||
gtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttg-acttaca---tgattgat-ttccttaa---cagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
------gtcagttaaaaata-gagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgttttta--tattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
      || | ||  ||||  | | |    |    | | ||  |||||| || | |     |  | |   |  |||   |||  ||| |   ||      || ||| | || |||||   ||||||||||| ||||| || ||||| |||||||| ||||| ||||||||||||||||||
gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgta-----tgtctctagtaattgaaattagctatcagttgacttacatgattggt-ttccttaa---cagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 4
gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgttttta--tattacacgagcactttggttgatgt-tacttaatc---acagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
                || |   ||  | | |    | |  | || |     |   ||   ||| ||||   |||  |  ||      || |||  ||   |  |   |||||   |||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||||
----------------gtcagtgtgaacgtgtctcatgttttgttggcttctat--actttgttttttggacttaactgataagtattcagtttacttatggaatgggtaatcttaacagGTGGAAACTTTTGGTGCCATGGCCAAGACTGAGAAAATTGCATTCATTCTCGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
gtcagt-taaaaat---agagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
|||||| | ||  |   | |  |    | ||||| |    |||| | || | |   |   |    ||  |  ||||   |||   | | | | | ||                 ||||||||||||||| ||||| ||||| || ||||| |||||||| |||||||||||||||
gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctga----------------acagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgtttt-tatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
            ||   ||  | |   | | |  |||      || |   | |         || ||| |||| ||  |||     |  | ||| |||   ||| | ||| | ||||||| ||||||||||| |||||||||||||| |||||||| |||||||||||||||
-----------gtaagcttttctt---cctctactttccaactttcgtggaaatcgtttt--ttatttattttatagtttatcaatgtgcattgattgtgatta-tgaattatagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcagttaaaaatagagttaccatgggctttt-tatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
                       |  | |||| |   |||||   |  ||    ||       || ||   || |   | || |  ||| |||| |  ||  |      | ||||||||| ||||||||||| |||||||||||||| ||||||||||| || |||||||||
----------------------gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgt---taacccctgcaatttgataaataat------taacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaa-acactaaccccgttg-------tttgtttttatatt--acacgagcactttggttgatgtta---cttaatca-cagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
                      ||   | ||    |  ||||  |      |  | ||  |||| |   | | |   |    |   |           | |  | ||||  | |   |  |  || ||  | |      ||  ||  ||||||||||| |||||||| |||||||||||||| || ||||| |||||||||||||||
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagta-acatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA

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|351035869|gb|FQ463714.1|FQ463714
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
EST: gi|110391070|gb|EC956024.1|EC956024
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
EST: gi|110381624|gb|EC934958.1|EC934958
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
EST: gi|27583566|gb|CB006261.1|CB006261
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
EST: gi|349825795|gb|FQ423090.1|FQ423090
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
EST: gi|161712574|gb|FC062176.1|FC062176
EST:     AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT
genomic: AAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaa ... ttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA
                                           acttaat  putative branch site (score: 4)
      tttgtttttatattac  TA-rich tract