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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG

Basic information

species Vitis vinifera
transcript Vv07s0191g00060.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 2
ctcaaagtcctcccaaaatttttcttattt-ttacccataaagtatcatcttgtactt-tacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
        |||  |||  | |  ||| ||   |    |   |  || |  |||   || | | |   |   |  | ||| ||   |  || | ||  |||||||| ||||||||||||||||||||||| |||||||||||||| ||||| ||||| |||
-gtgggtgcctttcaatgtctaccttgttagctgatgactgaacattagtttgagtttgttctgtaaaattggatatctgatgcctttgtat-gtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 2
ctcaaagtcctcccaaaatt-tttcttatttttacccataaagtatcatcttgtactttacag-----aggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
     ||  ||   | | || | | |   |||      | |  |||    |    || | | |     | | |  |   ||  |  |||    |    |  ||||| || ||||||| ||||||||||||||| ||||| |||||||| ||||| || || || 
-----agaactgttatagttatctgtccgtttggtgtgttatatatttgttcaagctctcctgttgtaatggtatgtaattagtgctttcctat-caattgtgcagCCGGGCATTTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 2
--ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatctt-gtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
    ||   |  ||  || |   || |||  |  | | |||   | |  ||||  | || |||   |  |    || |  ||    |   | |   | |  || || || |||| ||||   |||||||| |||||||||||||| ||||| |||||||||
attgcatccttttcttaacagagttattaaatcaaac-atatgcttttttcttcatgctctactt-gctttgatttctgataaacctttctatcaac-tatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 1
ctcaaagtcctcccaaaatttttcttatttttacccataaagt-atcatcttgtactttacagaggatcagcttttcttatt--------tttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
          ||   ||  |||| | |||| | || |  |||  |   |  ||| ||||   |      |  || |||| ||        |   |   |||   ||||| ||||||||||  |||||||||||||||||||||||||| ||||||||||| ||||||
---------ttcatgaagattttataatttgttcctaagaagccaattttatgttcttttgggcaatgtaatttgtcttgttaaaaatattcctatctttgatttgcagACGAGCATTTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 2
ctcaaagtcctcccaaaatttttcttatttttacccataaagt--atcat-cttgtacttt---acagaggatcagcttttctta---tttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
          ||   ||  ||   | |||| | || |  |||   ||  | | ||| ||||    ||  | || ||  ||  | |   ||| | |   |||   |  |||||||||||||  |||||||||||||||||||||||||  ||||||||||| ||||||
---------ttcatgaagattaaatgatttgttcctaagaagccaattttacgtgttcttttgggcaatgaattagtcttgttaaaattttcttaactttgatttttagGCGAGCATTTTGGGACAAGAGGATCTCACAGGAGGTCATCGGAGATGCACTCGGTGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 3
-ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
 | ||  |       |      |    || | |     | || | |    | ||  ||   |   | |   || || | ||  ||  || ||    ||||||||||||||||  ||||||||||||||||| |||||   ||| ||||| |||||||||
tcgcactggtaaataatgggactgggaatctgtgttgtttaaattttgattggt-tttgggacttgttttcctgttatgataattctgtttttaattgcagGCGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 2
-ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
  |    |         ||       | | |   ||| |    | ||   |      |     |   || | | || | ||| ||  |   | |  ||||| ||||||||||  |||||||||||||| ||||||||   ||| ||||| |||||||||
tttagcggggaaatttgaacccgcgatctctccccccttcccttctcccttcaccactggaccaacctctgttattgt-attcttatgctatatattgcagTCGAGCATTTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 2
-ctcaaagtcctc-ccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
 |||  | |  |    ||      |   | | |      |  ||| |    | ||  ||   |   | |   || || | ||  ||  || ||    ||||| ||||||||||  ||||||||||||||||| |||||   ||| ||||| |||||||||
gctcgcactggtaattaatgggagtgggaatctgtgttgtttagttttgattggt-tttgggacgtgttttcctgttataataattctgttttaat-tgcagACGAGCATTTTGGGACAAGAGGATCTCACAAGAGGTTGTTGGTGATGCTCTGGGTGAG

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|110406936|gb|EC972523.1|EC972523
EST:     CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACT                         GCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
genomic: CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACTgtaagaaatt ... tgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
EST: gi|351027768|gb|FQ446935.1|FQ446935
EST:     CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACT                         GCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
genomic: CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACTgtaagaaatt ... tgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
EST: gi|32269925|gb|CD719084.1|CD719084
EST:     CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACT                         GCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
genomic: CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACTgtaagaaatt ... tgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
EST: gi|110732898|gb|EE108585.1|EE108585
EST:     CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACT                         GCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT
genomic: CCTACGACAGGGTGTCAGAAAAAGCTCGAAATCGACGACGACCAGAAACTgtaagaaatt ... tgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG
                          ttttcttatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatcttgtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - -tcctccc
- - - - - - - - - - - - - - - - -cccataa