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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgcatcattctttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG

Basic information

species Vitis vinifera
transcript Vv14s0006g02020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 2
tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgca--tcattctttacaagcttttga-tgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
      ||  ||    ||||   |  | |  |  | | ||  |   ||   || ||    |  |||  |  | || | | | || |  | ||        |||||| ||||| ||||| | |||||||||||| ||||| || || || ||||| || |||||||| || || |||||||| || ||||| || |||||||||
--gtggtagcttatcatcttatatcaaaacaaaatat-tgtctggctgcttcttcaagctacccttggccggtttgtaactttgtatttcttgaaaaatgcagGTGCGTCAGATTTGCTAGTGAGGTTGCTGGTGTTCAAGACCTGGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTGGAGAAACTTATG

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 2
---tcacattaatttcaactcttgatttgagagtatttgtctggt--ttagtgaagctgcatcattctttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
   | |  ||  | ||| ||| || | |   |  |||  ||| |    | ||| |  | |   |   ||  |     | |||||     || |||       ||| |||||||||||||| |||||||||||||| ||||| || ||||| ||||| || |||||||| || || |||||||| || |||||||| |||||||||
tttttaatttgttgtcatctcgtgctgtagaacaattgttctcgcaacttgtgcaagttctgtaca-ttggctgatatgtgatgc---tatttttaaattg-cagATGTGTCAGGTTTGCTACTGAGGTTGCTGGTGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 2
--tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgcatcattctttacaagcttttgatgtgaacatgtttg-gtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
  | |||||   || |  || ||   | |  |  | | |||  ||  |  |||||   |   || |  |     | |||||  |   | |||        ||||||||| |||||||| |||||||||||||| ||||| || ||||| ||||| || |||||||| || || |||||||| || |||||||| |||||||||
tcttacattgcattgacatcatgtgctaaatggttctctctacttgtgc-aagctctgta--tcctggctgatatgtgatgctattttattttcaaattgcagGTGTGTAAGGTTTGCTACTGAGGTTGCTGGAGTTCAAGACCTTGGTATGTTAGGTCGTGGCAGTGGTGAAGAAATTGGAACATATGTTGAGAAACTTATG

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------tcacatta---atttcaactcttgatttgagagtatttgtct---ggtttagtgaa--gctgcatc---attctttacaagcttttgatgtga-acatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
                                                                     ||  |||   |||  || || |  | |||     ||  |||      ||| | ||    |  |||    | | | | | |  | || ||  |    | |||  | |||||||||||| || |||||||| |||||||||||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||| ||
gtcaatattggactaaactttatttttttccctgtaaatctgattattgtgaatgcagattttattaaacatgttacacattggaaatcatattatgacttatttcttctaaaaacttattaaatactttaatctgagtgcctgaaagggctctggtggaatgtttctttctttcaacagGTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGCAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTG

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgcatcattct-------ttacaagcttttgatgtga-acatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG-
                                                                       |   |   |||  || || |  | |||   ||||| |  |    |    |  | | | | |||       | | | |  | || ||  |    | |||  |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| || ||||| || |||||||| ||||| || ||||||||||||||| || 
tcaatattggactaaactttcttttttccccctgtaaacctgattattgtgaatgcagattttattaaacatgctacacattggaaatcatattatgact-tatttcttagaaaaatatcaattactttaatctgagtgcctgaaagggctctggtggaatgtttctttcttccaacagaTGTGTTAGATTTGCAACAGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTAGGTCGTGGAAGTGGAGAGGAGATTGGAACATATGTTGAAAAACTTTTGA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 2
tcacattaatttcaactcttgatttgagagtatttgtctggttta-gtga-agctgcatcattct--ttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
     ||| |   |    ||| ||  || ||  |  | | ||| | |||| || | |   || ||  | |  || ||||| | || | |    || |     ||||||||  | |||||  |||| ||||||||||||||||||||||| ||  | || ||||| || |||||||||||||| |||||||||||||| ||||||
----gttactaatatagtttgcttatagtgtgatgttttagttaatgtgatagatacgctatcctgttgattaggttttg-tatgtataa---tgtttttgtagGTGTGTACGATTTGCTTCTGAAGTTGCTGGGGTTCAGGATCTTGGTATACTAGGTCGTGGTAGTGGAGAGGAAATTGGAACTTATGTTGAAAAGCTTATG

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|56409648|gb|CX017900.1|CX017900
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
EST: gi|110731198|gb|EE109146.1|EE109146
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
EST: gi|352781338|gb|FQ467784.1|FQ467784
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
EST: gi|110732595|gb|EE108017.1|EE108017
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAAGTTTGCAACTGA
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGA
EST: gi|161712112|gb|FC061484.1|FC061484
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
EST: gi|110723230|gb|EE100308.1|EE100308
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAAGTTTGCAACTGAGGTTGCTGGGG
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGG
EST: gi|110688867|gb|EE067907.1|EE067907
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAAACTGAGGT-GCTGGGGNTCAAGATCTTGGCATGT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAA-CTGAGGTTGCTGGGGTTCAGGATCTTGGCATGT
EST: gi|352772818|gb|FQ473856.1|FQ473856
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
EST: gi|110699724|gb|EE076975.1|EE076975
EST:     CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACG                         GTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT
genomic: CTTGGCCCTTTGGTTAAGACTGTGATGACTCGTTGCATTCAGTGTACACGgtatgaatgt ... ggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagctgcatcattctttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG
                          ttttgat  putative branch site (score: 4)
             attcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacattaatttcaactcttgatttgagagtatttgtctggtttagtgaagctgcatcattctttacaagcttttgatgtgaacatgtttggtccaacagGTGTGTCAGGTTTGCAACTGAGGTTGCTGGGGTTCAGGATCTTGGCATGTTGGGCCGTGGCAGCGGAGAGGAAATTGGGACTTATGTTGAAAAACTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - caactct
- - - - - - - - - - - - - - - - - tgtctgg
- - - - - - - - - - - - - - - - - - - - - - - tgaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacatg