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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA

Basic information

species Vitis vinifera
transcript Vv18s0001g00190.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 4
gtaggaacatattttaagata-ttttgctctccccaagtgtggagtcccatgcgattcatcacctt--accaagattgaacatttttggtgtt-tcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
         ||   |  | |  |||||||   |  || |        | || ||    |||    |  |          | ||||||  | |  |    | |||||||||    ||||| ||||| || ||||| || || ||| | |||||||| || ||||||||| | ||||||||||| || |||||||| | ||||||||
-----tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 4
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcacc----ttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
||| |  |||    ||  | |  ||| |  |    |   || |  |   ||   |||| ||||    |    | |  | | | | |    || ||  || | |||||||||||||| || || || |||||||||||||| ||| ||||||||||||||||||||||  |||| ||||  |||||||| || || |  || || |
gtatgc-catgacctataacagattgatgccttttacaatgtaaacg-gtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacg-cagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCGGAAGTGAGGGAACTGGTAGAGAGAGCATATTCTAGGGCAACACATATTA

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 4
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaa--gattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
||| |   ||    ||| |||  ||| || |    |   || |  |   |||  || | ||||  |  |   |  ||| |||||    || ||  |||| |||||||||||||| || || || |||||||||||||| ||| ||||||||||||||||||||||  |||| ||||  |||||||| || || |  || || |
gtatgc-tatgacctaaaataggttgatcccttttacactgtaaacgt-tgctcttgaacaccaaaatatatgcctgaccatttcaaatgattgtaatg-cagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCGGAAGTGAGGGAACTGGTAGAGAGAGCATATTCTAGGGCAACACATATTA

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
         ||| ||  | | | | | | ||  ||   | |  ||    | |||    |     |   |    |  | ||   ||   | |    | |||||||||||| |||||||| || || ||||||||||| ||||| || ||||| || ||| | ||||| || |||||||||||    ||||| | | ||||||
--------gtatatt--gctttctcggtttcatcattagggttgttg-gttcgacaagttggagtgttacttatatatatccgtgaaatgttt--ttgcagATGTCATCACAGAAAGATTACTCAATGGCAACTGCGGATATTGTAGATGCTGAGGTGCGAGAGTTAGTTGAGAAGGCATACAAGAGAGCAACGGAGATCA

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
||| | | |||      |||| |  | | | |  || |      |    ||   ||     |  |  |||     ||||| |||  |||||      |||||||||||||||||| || || || |||||||| || ||| | || |||||||||||||| ||| | || |||||||| ||    ||||| ||  ||||||
gtaagtatataaaactcgatactcaggttttcataatt------tattgtgttgtttccagctct--caa-----aacatgttt--tgttt------gcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA

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|110391145|gb|EC956102.1|EC956102
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
EST: gi|110717414|gb|EE093251.1|EE093251
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
EST: gi|26262505|gb|CA813568.1|CA813568
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
EST: gi|26262506|gb|CA813569.1|CA813569
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
EST: gi|352790761|gb|FQ478309.1|FQ478309
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCC
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCC
EST: gi|352794299|gb|FQ481530.1|FQ481530
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACT
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACT
EST: gi|37183867|gb|CF603221.1|CF603221
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGAT
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGAT
EST: gi|30320659|gb|CD003921.1|CD003921
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
EST: gi|352798544|gb|FQ480569.1|FQ480569
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAG                         ATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacat ... caaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA
              accttac  putative branch site (score: 3)
                             aacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA