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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctgcttctcacttcctactatgtctcttttgtttctctcattgggatttgatttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA

Basic information

species Vitis vinifera
transcript Vv02s0012g02570.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g02130.1 (Oryza sativa), 3'ss of exon 7
atcctgcttctcacttcctactatgtctcttttgtttctctcattgggatttgatttatgatcatggaattgagaatgtgtccatgttctgtt--ttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
     |      || | || || ||  |    || || | |  |||   |  ||   | |  |  | ||   |   | |   ||  || | ||  ||   ||||| || || || || |||| || |||||||||||  ||||| ||||||||||||||||||||||| |||||  |    ||| | ||||  ||  | || 
-ataggtaggctacctgct-ctttgcttggggtgattatttatttgccctgcgaagcaagtaccggaaagctattgtctcatcagcttttattccttttcagATATCAGCTGATTAGAGTAAGTGCCAAGGGAATGAATGAGGGATGCAAGTGGGTGGAAATGTTTGAGGATGTCAGCATGGTAATATTCTCGGTAGCACTC

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os11g10050.1 (Oryza sativa), 3'ss of exon 7
atcctgcttctcacttcctactatgtctcttttgtttctctcat-tgggatttgatttatgatcatg-gaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
                     ||  ||||||   ||  |  ||| ||  | | ||| |     |||| | | | |   |   |  ||||| || |   | ||||| ||  | || || |||| || |||||| ||||  || || ||||||||||||||||||||||| ||||| ||    ||  | |||| |||  |||| 
--------------------gta-atctcttaacttcatgccatgtgcaaatcgatct-cagccatgtgcacttaatgttcttatatgttttgctcctc-agATATCAGTTGATTAGAGTAAGTGCCAAGGGCATGAATGATGGCTGCAAGTGGGTGGAAATGTTTGAGGATGTCCGCATGGTGATATTCTCTGTAGCCCTC

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G429113_T01 (Zea mays), 3'ss of exon 7
atcctgcttctcacttcctactatgtctcttttgtttctctcattgggatttgatttatgatcatggaattgaga-atgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
            ||   |||   |  |   | || |   ||   | | |||     | |  |  | |  |||    || ||    | | || | |    || ||||| || || || || |  | |||||| |||| |||||| |||||||||||||| |||||||| |||||| |    ||  | |||| |||  | || 
----------gtacagtctatcttccccgctctgctcacctg--tcgaattcttcctctcctagttgtcttgcctcatatgcttctatcctctctc---agGTACCAGCTGATTAGAGTGAGCGCCAAGGGCATGAACGAGGGCTGCAAGTGGGTGGAGATGTTTGAGGATGTTAGCATGGTGATCTTCTCTGTAGCGCTC

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G016858_T01 (Zea mays), 3'ss of exon 7
atcctgcttctcacttcctactatgtctcttttgtttctctcattgggatttgatttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
                      ||   |  ||   ||  ||  |  | |  ||  | |  |  ||| |  ||| |   ||| |   || |  ||    ||||| || || || || || | ||  || || ||||  || || ||||| ||||||||||||||||||||||| ||    ||| | ||||||||  | || 
-------------------gtaataatttcttaacttgccttgt--gaacgtgtgtaaaaaaaatgcatctga-atcatgtgctcttttttattcatcagATATCAGCTGATCAGAGTCAGTGCAAAAGGCATGAATGATGGCTGCAAATGGGTGGAAATGTTTGAAGATGTCCGCATGGTAATATTCTGTGTAGCACTC

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G34300.1 (Glycine max), 3'ss of exon 8
atcctgct-tctcacttcctactatgtctcttttgtttctctcattgggatttg--atttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
    |||| || |  || |    |  |  |       ||   || ||  ||||   |  |   || |   |    |  |     || |  | || | | | || || ||||| |||||||| |||| ||||||  |||  ||||| ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||||
---ttgctatcaccattgccctcaccttccccccacctcatacactgaaatttagaaactgaaatgagaaacgcaaagactaaacccttctttgatgtcccagGTATCAACTCATAAGGGTGAATGCCAAGGGCCTGAATGAGGGCTGCAAGTGGGTTGAAATGTTCGAAGACGTTCGAGCAGTGGTCTTTTGTGTTTCCCTA

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G01470.1 (Glycine max), 3'ss of exon 8
atcctgcttctcacttcctactatgtc-tcttttgtttctctcattgggatttgatttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
  | |  || |   |  |  |  | || ||   |  | | | | |     |  ||   |  |    | ||   ||| |    || | || || | |   || || ||||| || ||||| |||| ||||||  | |  ||||| || |||||||| |||||||| |||||||||||||| || || || || |||||||||
ggctttattgttgttatcgtcagtatcctcaccttctccccacctcacactgagaaacagaaatgagaaacacagactaaacccttctt-tgatgtctcagGTATCAACTCATTAGGGTGAATGCCAAGGGCCTAAATGAGGGCTGTAAGTGGGTTGAAATGTTCGAAGATGTTCGAGCCGTGGTCTTTTGCGTTTCCCTA

upper sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 8
atcctgcttctcacttcctactatgtctcttttgtttctctcattggga--tttgatttatgatcat-ggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
                        |||  ||     || || ||| | |   ||||      | | | || | | |  || | || ||  | |   |||| || ||||| |||||  | ||||| |  |||||||||| |||  | ||||| ||||| ||||||||||||||||| ||||| ||  | |||||  |   | ||
------------------------gtcggttaacactcacttattcgcaatcttgaaccgcaagctttggtacttattattt-tcaatcctttccgttgc-agGTACCAGCTTATCCGCGTAAACGCAAAGGGAATGAACGATAGCTGCAAATGGGTAGAAATGTTTGAAGATGTACGAGCAGTCATCTTCTGCATCAGCTTA

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|34549410|gb|CF517642.1|CF517642
EST:     TCTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAA                         ATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
genomic: TCTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAAgtaatttctt ... gttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
EST: gi|34549495|gb|CF517727.1|CF517727
EST:     AGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAA                         ATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
genomic: AGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAAgtaatttctt ... gttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
EST: gi|110688691|gb|EE067531.1|EE067531
EST:     TCTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAA                         ATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
genomic: TCTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAAgtaatttctt ... gttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
EST: gi|110691075|gb|EE068761.1|EE068761
EST:     CTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAA                         ATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG
genomic: CTGAAACCTACACAGACAATCAGGAAGCTCCATTGCAGCCTGTGACTAAgtaatttctt ... gttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatttgatttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA
   atttgat  putative branch site (score: 5)
                                         ttctgtttt  putative PPT
     ttgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctgcttctcacttcctactatgtctcttttgtttctctcattgggatttgatttatgatcatggaattgagaatgtgtccatgttctgttttgctagATACCAACTTATAAGGGTAAATGGCAAGGGAATGAGCGAGGGTTGCAAGTGGGTGGAAATGTTTGAAGATGTTCGAGCTGTAGTGTTCTGTGTTTCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- cctgctt
- - - - - -cacttcc
- - - - - - - - - - - -tgtctct
- - - - - - - - - - - - - - - - - - -ctctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt