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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgaataatcatgatataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA

Basic information

species Vitis vinifera
transcript Vv07s0130g00270.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------ccttgaataatcatgatataggttcctatctgttt-tctgttagt---------cgttattaatgcttcattcttt--ttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
                                                  | ||||  ||   |    |   ||| | | | ||  |||| |  |           ||||| |    |  | | |   ||| || |||  ||| | ||   |  ||  | ||||||| || || || ||||||||||| ||| | ||||  ||||||||| ||||||||||||| |||||||| || || |||||||| |||||||| ||||
gtattaagactgtataagataacatataaggctactgtgttctccttttgctttgagcaaaatttcagtgctttcttttgttttaatctgctgatgtaaaaaccttttattgaccactgctccatagattgtttgcttagtttgtattacatgctttgc-agAAAGGTGGTGGTACTATTGATCTTGAGCCTCGCCTAAGCCATACATCAGCTGTGGAGCCTACACTTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 6
-------------------------ccttgaataatcatgatataggttcctatctgttttctgttagtcgttattaatgctt--cattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
                            ||  |  || |  | | | ||| |   |   || ||  |     || | ||  ||      |    || || |||   |||||||   || ||  | ||||||| || || |||||||||||||||||  | || |  || |||||| ||||||||||||| ||||||||||| || |||||||| |||||||| ||||
gcaagggtgtgacagtgtagagcattactgtgtc-tcctttttttgattcatggttaccttttgaaaccttatactgattattgttgcacaggatgtttgcttagcttcttttacattatttgc-agAAAGGCGGTGGCACCATTGATCTTGAACCACGCCTTAGTCACACATCAGCTGTGGAGCCTACACTTGCTCCAGTTGCGGTTGAGCGCACAATGACGACAA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 7
----------------ccttgaataat-catgatataggttcct-atctgttttctgttag--tcgttattaatgcttcattc-------tttttgct-tcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
                        | |  |  | |||   |  | || || || |  | ||   | || |    |||  |||        | |||||| | |||    ||||||   |  || |  ||||||| || || ||||||| |||||| ||  | || |  ||    ||| |||||||||||||||| || ||||| || ||||||||||||||||| ||||
gtatgaactatgaaggatgcagccagtatagaacatacacttttgatgtggttaccttcaggaacattttactggctctatttcatggaatgtttgctatgcttagcatcttttacatgctttttcagAAAGGTGGTGGCACCATTGGTCTTGAGCCACGCCTTAGCCACGTGTCAGCTGTGGAGCCTACTCTCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 6
--ccttgaataatcatg-atataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
    ||  ||   |||   ||||  ||  |   || ||     | |    ||| ||   |  |  |||  |  ||   || |   ||| ||  | |||   |||||||||| || || ||||||||||||||||| || ||||||||||||||| | ||||| || |||||||||||| |||||||||| || |||||||| |
acatttacatggacatatgtataaatttattattggttgaacctggcacctatcaacattaaaaacttaatatttaacttctcattttgttgatcttc---agAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 6
ccttgaataatcatgatataggttcctatctgttttctgttagtcgttat-taatgcttcattctttt--tgcttcctttttttcttttttctttt-tctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
  || |    ||   || |  |||| |      ||       ||   |   ||||| |  | | |  |  || ||| |    || || |||||||  |||  |||||||||| || || ||||||||||||||||| || |||||||| |||||||| |||||||| ||||| ||||||||| ||||||| ||||| ||||| |
--tttacctgtct--attttcgttcattctcaattggacaaggtaactgcataatgttaaaatttaatggtgattcttaccgtttttatttctttggtcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACCTCAACTGTTGAGCCTACCCTTGCACCAGTGGCTATTGAGCGGACAATTACTACTA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 7
--ccttgaataatcatg-atataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
    ||  ||   |||   ||||  ||  |   || ||     | |    |||  ||  |  |  |||  |  ||   |     || |||| ||  |||  |||||||||| |  || ||||||||||||||||| || ||||||||||||||| | || || || |||||||||||| |||||||||| ||||||||||| |
acatttacatggacatatgtataaatttattattggttgaacctggaatctatctatattaaaaacttaatatttaactgc---ctattttgttgatcttcagAAAGGAGGTGATACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAACCCACCCTTGCTCCAGTGACTGTTGAGCGGACAATGACTACCA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 5
ccttgaataatcatgatataggttcctatctgttt--tctgttagtcgttattaatgcttcattcttttt---gcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
    |  |  | |  |  | | |   | ||  ||      | ||   |  || |||  || |  |||  |   | |||    |  | | |||  ||  |||  |||||||||| || || ||||||||||||||||| || |||||||| |||||||| |||||||| ||||| ||||| |||  |||||| ||||| ||||| |
----gtctgtttacaagttcgttcattctcaattgaactaggtaactgc-ataaatatttaaaacttaatggcgattctgactgctttatttctttggtcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACCTCAACTGTTGAGCCTACCCTTGCACCAGTTGCTACTGAGCGGACAATTACTACTA

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------ccttgaataatcatgat-ataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttt---tcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
                             |  |||   | |||| ||    ||| |     |   |  ||     | |||| |     || | |     ||||| |     |  |  |  | |   || |||||||||| ||||| ||||| || |||||||  || |||||  | |||||||||||||| |||||||| ||| ||||||||||  |  | ||||| || |
gtgatttgacatgtgccattatgtgtctttctaatttccttgattatcttctcccactatgtgcgtaatatctagttttaa-gtgaatttgtgtaaaactccttatggaaattctgatgatatgattccagAAAGGAGGTGGGACTATTGAACTGGAACCTTCCCTTACACACTCCTCAACTGTGGAGCCAACTCTTGCACCAATGGCTGTTGAAAGATCTATGACCACCA

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|110420000|gb|EC986260.1|EC986260
EST:     AGCTACCGTGTCGAACGGTGCTGCATTGTGAAG                         AAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACT
genomic: AGCTACCGTGTCGAACGGTGCTGCATTGTGAAGgtgataaaca ... ttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACT
EST: gi|110717059|gb|EE092582.1|EE092582
EST:     CAATTGGTTGTAGCTACCGTGTCGAACGGTGCTGCATTGTGAAG                         AAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACT
genomic: CAATTGGTTGTAGCTACCGTGTCGAACGGTGCTGCATTGTGAAGgtgataaaca ... ttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA
  tattaat  putative branch site (score: 2)
               ttctttttgcttcctt  putative PPT
                             tttttttcttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgaataatcatgatataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
ccttgaa
- - - - - - - - - - - - - - - - - - ctgttag