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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatatccttttttgtcttcaccctttttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaattttgtcattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA

Basic information

species Vitis vinifera
transcript Vv13s0019g04680.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 5
-agatatccttttttgtcttcaccctttttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaattttgtcattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
 ||  |   | |    | |  ||  || | |  | ||  ||  || |   | || | || |    |        |   || |   |||| | || || |||||| | ||||||||||| || ||||||||| |||||| ||| ||||| || ||||||||||| ||||| |||||| | ||| |   ||| 
cagtgagattgtaccatgtcgactattgtgaagt-atgttatgtttccacttcttttttcaggtatgaagcactttcagattgttttttcttatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 5
--agatatccttttttgtcttcaccctttttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaattttgtc--attttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
  |||||     |||| | |  | | |        |||| ||  ||    ||   || ||   ||| |    || |||  | |||| | |  |  |||||  ||||  | ||||||||||||||||||||||| || |||||  | || || || ||||||||||||| |||||| || |||||  | || || 
ttagataggagcttttttttatagcatag--gatctatttta--ttaggatttacattttctgtctattttgttttagcaacttaaatattactaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 5
agatatccttttttgtcttcaccctt---tttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaa-ttttgtca-ttttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
   |||    | || |    ||| ||   |      |||| ||  |    | | | || ||   ||| |  | || |||  | | || | || | | ||||  ||||  | ||||||||||||||||||||||| || |||||  | || || || |||||||||||||  ||||| || |||||  | || || 
---tatgacatgttataaaaaccattagataggagctatttta-ttaggagctac-attttctgtctatttcattttagcaactgaaatattattaattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAATAAAGCTGATCTTCTCGAGAAGCGGGAAGTTGCTGTCCAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 5
agatatccttttttgtcttcaccctttttaccttattctaacttcctgttgctatgttgaatctt-tccctttatagtgaattaattttgtcattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
 | || | |        ||  | |   |      |    |  |  |      ||| ||||||||  | |  || |  |              || | ||||||| ||||||| ||||||||||| |||||||| |||||| | ||||| |||||||||||||| ||||| ||  ||||||||||   | | 
tgctaccatgaagccatttggcacaactccgtgcaggaaagatatcaac-attatattgaatctagtgctattgttttacccctgcccataaatctaacagGAACTGCAAAAGCATGGAAGCCCAGATATTGTTATGGCTCTGGTTGGTAACAAAGCTGATCTACATGAAAAAAGAGAAGTACCTACTGAG

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|294963923|gb|GW836798.1|GW836798
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGAAAAAACATGGAAGCCCTGATATTGTCATGGCTTT
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTT
EST: gi|351049141|gb|FQ449863.1|FQ449863
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351031329|gb|FQ445354.1|FQ445354
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110378503|gb|EC943640.1|EC943640
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110386522|gb|EC951122.1|EC951122
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110707796|gb|EE084605.1|EE084605
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351029650|gb|FQ427490.1|FQ427490
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351031354|gb|FQ445379.1|FQ445379
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351036602|gb|FQ457315.1|FQ457315
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110390981|gb|EC955931.1|EC955931
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351033397|gb|FQ462048.1|FQ462048
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|30302011|gb|CB978805.1|CB978805
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|349830843|gb|FQ418151.1|FQ418151
EST:     TGATATAACAAGCCCAGAATCATTCGAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: TGATATAACAAGCCCAGAATCATTC-AACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110428129|gb|EC994591.1|EC994591
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|351016862|gb|FQ424289.1|FQ424289
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
EST: gi|110691925|gb|EE070587.1|EE070587
EST:     ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAG                         GAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC
genomic: ATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatcttttt ... cattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgctatgttgaatctttccctttatagtgaattaattttgtcattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA
                                 aattaat  putative branch site (score: 3)
                                       ttttgtc  CT-rich tract
                        tttatagtgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatatccttttttgtcttcaccctttttaccttattctaacttcctgttgctatgttgaatctttccctttatagtgaattaattttgtcattttacagGAATTGCAAAAACATGGAAGCCCTGATATTGTCATGGCTTTAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - -caccctt
- - - - - - - - - - - - - - - - - - - - - - cctgttg