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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatccttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT

Basic information

species Vitis vinifera
transcript Vv05s0077g02310.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 14
gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatccttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT
                                              | |||  |  ||   | ||||  || |  | |  | | |    | | |     || || | | | | ||     |||| | || | |||| |  | ||||||||||||||||| ||||| |||||||| ||||  || || ||||| |||||| | ||||| |||||
----------------------------------------------gttagtttcaat---gccattaaattttca-tactatctagtatctaccctgctggaaataattataatt----ttttttcttgtgcagGAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 12
gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatccttgaaagttaatgtcatcgttc--ttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT
                                                           || |  || ||| ||| | |||| ||| |  | |   |    |   |      | |  |        | ||||| |||| |  | |||||||| |||||||| |||||| ||||||| ||||| ||||| ||||| |||||| |||||||||||||
-----------------------------------------------------------gtaattttttat-tcatgatttgattttcaatattgactacaatgttatggacccttatatagcaacccttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatccttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT
                                                     |||  |      ||  | || |   |||    |  |  | || |||    | ||||||||    |  || | |||  | |||| ||  |||||  |||||||||||||||||||| ||||| ||||  ||||| || || || ||||  |||||||||||
-------------------------------------------------gtaattgtcttgctttttcaaccttagagttttgcatgataatgcaccct---gatttaatgtc----tctttctgtttcgttcagGAATGATTTTGTTTCTGCATCAGCTGACAACATCAAGAAGTTTAGCCTTCCTAAGGGAGAGTTTTGCCACAACATGCT

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatcc-ttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT
              |||   | | ||  | ||  |  | |   | |  | | | ||| | | || || | | || | |   |   || ||   | |    |     || |||| |||  | |  | || |||  ||| || | ||||| |||||||||||||||||||  ||||||||||  ||||| || || || || |  |||||||||||
------------gtatgtgtagtcgt--actgaatctacttttgtgtatcgtgctgaatct-actttatctttccaatagcgaagtctttgcacctaaacttttcctttatgttatctctttaattttctttttagGAATGCCTTTGCTTCTGCATCAGCTGACAACACCAAGAAATTTAGCCTTCCAAAGGGAGAGTTCTGCCACAACATGCT

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|110416775|gb|EC982779.1|EC982779
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|77578499|gb|DV218043.1|DV218043
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCA
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCA
EST: gi|254917683|gb|GR903335.1|GR903335
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|349818063|gb|FQ408838.1|FQ408838
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|351038798|gb|FQ464664.1|FQ464664
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|110384526|gb|EC948969.1|EC948969
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|110724126|gb|EE099691.1|EE099691
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|110418369|gb|EC984516.1|EC984516
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|110418288|gb|EC984425.1|EC984425
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCC
EST: gi|161707291|gb|FC057696.1|FC057696
EST:     CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGA                         GCATACTTTTGCATCTGCATCAGCTGACAACATAAAG
genomic: CTCACACACCATAAGAAATCTGTGAGGGCAATGGCACTGCATCCTAAAGAgtatgccctt ... ttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcctttttcatccttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT
                       agttaat  putative branch site (score: 4)
                             tgtcatcgttcttttc  CT-rich tract
                                     ttcttttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcccttgtacatgatcatttgttcattgtgtgaaataacggggctagggttgattgtgacattgtatctcaagttttgttttcctttttcatccttgaaagttaatgtcatcgttcttttcttttttccagGCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA