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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaataataatgtgtacacacaaaaatactccattgacacagaattttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA

Basic information

species Vitis vinifera
transcript Vv17s0000g00500.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 11
tttaataataatgtgtacacacaaaaatactccattga-cacagaattttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA---
         | ||  | |       |||  ||   ||  |||| |  |||    |   | ||  ||   |  || || |   |  ||     |    ||||||||||||| |||||||||| || |||| ||| ||||| |||||||| |||||    |||  |  |||| ||     ||   | || ||||||| || ||   
------gtgagtgctttcgtttgttaattttcggctgttcacatatgtttaaacg---gattccaattcacattgttctc--atgtttgtaatccactcagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAGTACTTCCCTGCGGAGCCGCCAAAG--ATTGCTGAAGCTGATCACGAT-AAGCTGGAGTAAATGATGA

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G030862_T01 (Zea mays), 3'ss of exon 10
-------------------tttaataataatgtgtacacacaaaaatac-tccattgacacagaattttggtagtgtggttgtaaccaattttcttattggac--cttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA----
                   |||     |    |||| |  |     |   | | ||| |||| | | |   ||| |  |   | ||   ||| ||   ||  |  |  |    | ||  |||||||||||| ||||||||||||| |||| ||| ||||| ||||||||  | |     |||  |  |||| ||   | ||  |   || ||  | |  |||    
gtgagcgttaatttttttttttgggtctctgctgtaaatgcttcgttttattcgttggcacata-tataaatagagccgaactgacgtgtttcctgtctgtgcaacccccatatattaccagGTTATCAGCAGAGTTGGTGACCTCGTGGGCATCAAGTACTTCCCTGCACAACGACCAAAG--ATTGCTGAAGCTGGTCACGGC--AATTGAGGCGGTAGAGAGG

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
tttaataataatgtgtacacacaaaaatactccattg--acacagaattttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA---
            |||       | ||||||| ||||   |  |      |    | |   |  | | |  || |  || |||    | |       | ||||||||||||| ||||||||||||| |||| ||| || || |||||||| ||  |    |||  |  |||||||     ||   | || |||||||   |     
------------gtgagtgt-tataaatacttcatttttattctaggagtcataaataaagccg-agctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAG--ATTGCTGGAGCTGATCATGAT-AAGCTGGAGTAGGAATCAA

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|71872282|gb|DT021337.1|DT021337
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCCATAA-GTATTTCCCTGCTGA
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCC-ATAAAGTATTTCCCTGCTGA
EST: gi|71866164|gb|DT015219.1|DT015219
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTAT
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTAT
EST: gi|110360549|gb|EC923744.1|EC923744
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|34542727|gb|CF510959.1|CF510959
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|22015490|gb|BQ800524.1|BQ800524
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|110421496|gb|EC987793.1|EC987793
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|34416104|gb|CF414858.1|CF414858
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|45368189|gb|CK906548.1|CK906548
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|110385601|gb|EC950143.1|EC950143
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|30124998|gb|CB910337.1|CB910337
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|110366510|gb|EC930420.1|EC930420
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|34320121|gb|CF372875.1|CF372875
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|110697624|gb|EE074785.1|EE074785
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
EST: gi|30255672|gb|CB971804.1|CB971804
EST:     TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAG                         GTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG
genomic: TCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAGGCTTAGAGgttgttgttt ... tttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA
              ttgtaac  putative branch site (score: 2)
                                             tttttgtc  putative PPT
                      aattttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaataataatgtgtacacacaaaaatactccattgacacagaattttggtagtgtggttgtaaccaattttcttattggaccttctggtttttgtcagGTTATCAGCCGAGTTGGTGACCTAGTGGCCATAAAGTATTTCCCTGCTGAGCCCAGGAAGCAACAGCTGGAGGAAGGCAGAGTGAAACTGGAGTGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- -aataataa
- - - - - - - -tacacac
- - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - -ctccatt
- - - - - - - - - - - - - - - - - - -acacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctgg