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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatgtcattggaaattttcttgttctagagcatagaaacataagagtcctctggttttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG

Basic information

species Vitis vinifera
transcript Vv04s0008g07000.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g55000.1 (Oryza sativa), 3'ss of exon 2
ttaatgtca-ttggaaattttcttgttctagagcatagaaacataagagtcctctggttttggtcac--accaacttactaatgctagaccaccc-tagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG
  |   |||     |  || | ||| |  |  | ||  ||     |||       | |  | || ||  || || | ||||||   |  |  ||| |||||||||| |||||||| ||||| ||||||||||| || ||||| |  ||||||||||| || ||||
--accatcaaccatattttctgttggttaatggaatgtaatgtccagaacataaggttcattgttaccaacaaattaactaat--caatctgcccatagtgcagATGTGCAAGTTTTTTCTCCAGCAACGATGTCGGTTTGGTAGTAACTGCCGCTTGTCCCATG

upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
-ttaatgtcattggaaattttcttgttctagagcatagaaacataagagtcctctggttttggtcac--accaacttactaatgctagacca-ccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG
  |    | |||     | | |||| |       ||| ||  ||  ||||      |   |  | |   || |||| |||||| | |  |   || |||||||||||||||||||||| |||||||| ||||| |||||||| |  ||||||||| | || ||||
tctggcataattt----tctgcttgctaacacaaatataatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG

upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 2
--ttaatgtcattggaaattttcttgttctagagcatagaaacataa-gagtcctctggttttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG
  |||| ||  ||      |  |   || | |  |  |   |   ||  |   |  | | |||  ||| | ||   ||||||| ||||| ||||  ||||||||| |||||||||||| |||| |||||||| |||||||| |  ||||| ||| |||||||||
ctttaacgttgttattc-ctcccaaattttggttccaaattattcaataaaatcaattgcttt--tcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG

upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G10210.1 (Glycine max), 3'ss of exon 2
ttaatgtcattggaaattttcttgttctagagcatagaaacataagagtcctctggtt-ttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG
    |  |||||  | |  ||      |   |     ||  ||   |         ||  |  ||  | ||   ||||||| ||||| | ||  ||||||||| |||||||||||| |||| |||||||| |||||||| |  ||||| ||| |||||||||
-ccttaacattgttattcctcccaaattttggttccaaattattcaatcaaatcaattgcttttcttatcattgtactaatactagaacgccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG

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|37186604|gb|CF605957.1|CF605957
EST:     TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTG                         ATATGCAAGTTCTTTCTA
genomic: TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTGgtacgtgcaa ... cctagtgcagATATGCAAGTTCTTTCTA
EST: gi|110712504|gb|EE090201.1|EE090201
EST:     TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTG                         ATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC
genomic: TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTGgtacgtgcaa ... cctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC
EST: gi|110718718|gb|EE095871.1|EE095871
EST:     TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTG                         ATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC
genomic: TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTGgtacgtgcaa ... cctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC
EST: gi|37190291|gb|CF609640.1|CF609640
EST:     TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTG                         ATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCAC
genomic: TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTGgtacgtgcaa ... cctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCAC
EST: gi|110702309|gb|EE080873.1|EE080873
EST:     TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAAAATGTTG                         ATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC
genomic: TGGACTCTGCAAAGATTTCTTTCCTTTCACCCACATCTGAAAATATGTTGgtacgtgcaa ... cctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtcctctggttttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG
                            tactaat  putative branch site (score: 1)
                                         ccaccct  putative PPT
                           ttactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatgtcattggaaattttcttgttctagagcatagaaacataagagtcctctggttttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG

- - - - attggaaa
- - - - - - - - - - - - - - -gagcata
- - - - - - - - - - - - - - - - - - gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgc