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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttggttgccacccatattagttcatttgtttttccctgttttgctttgttgaaaaacccctgataggaagatgatgtagcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGTTAGCAACAGCTGGTGGGAACCATGATTCTGGAAACAGGCCACTTATGTA

Basic information

species Vitis vinifera
transcript Vv00s0652g00030.t01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 52
---------------------gtaattttggttgccacccatattagttcatttgtttttccctgttttgctttgttgaaaa---acccctgataggaaga------tgatgtagca------agtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGTTAGCAACAGCTGGTGGGAACCATGATTCTGGAAACAGGCCACTTATGTA
                      |  || | ||| ||  | |  | |      | |  ||        ||   ||| | || |   |   ||  | || ||       |||| |   |      | |  ||  |   | || || |||||||| || |||||||||||||||||||||||    |   |||||||    |||                             
ttgctgacagttttttctagtttggttatagtttccgtctacttgaaccagatggagttgttaaaaattagcttgataaagatttagttctttttggcagGCCCTGGTGATTTGAAACCCCACAATCAAGCCATAGGAGGCACTTTAGATGCGATAAGGGAGAGGATGAAGAGCATCCAAGCTGGCGCAGCTGG-AACAAC-----------------------------

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 3'ss of exon 52
-------------------------------gtaattttggttgccacccatattagttcatttgtttttccctgttttg--------ctttgttgaaaaacccctgataggaagatgatgtagcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGTTAGCAACAGCTGGTGGGAACCATGATTCTGGAAACAGGCCACTTATGTA
                               || ||| ||    | | |   |||  || |  | | |  |    ||  |         ||| |||   |    ||| |     ||  |   |  || |  ||  ||  | || ||  ||||||| || ||||||||||||||||||||||||   | | | |||||  | |||                             
tggctttacataaactggctacttcttgcatgtgattctgagcac-agctggattgcttaaaatttctcgcgaaattcagagcgccttttttattgtgcagGTTCTGGTGATTGGA-AACCCAATAA-TCTAGCTACGGGAGGCACTCTAGATGCAATAAGGGAGAGGATGAAGAGCATCCAGGCTGGAGCTGCTGG-AGCAAC-----------------------------
















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|110368064|gb|EC932026.1|EC932026
EST:     GCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAGCAAGTGCAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAG
genomic: GCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTC-----C--G-G-AGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAG
EST: gi|110375502|gb|EC940491.1|EC940491
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|110389750|gb|EC954613.1|EC954613
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|30301267|gb|CB978061.1|CB978061
EST:     GTTTCGGCAGCATTTGAGCGACCAAAGGAATGAAAGGTTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|30299345|gb|CB976139.1|CB976139
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|110393973|gb|EC958256.1|EC958256
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|71882640|gb|DT031695.1|DT031695
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|30301485|gb|CB978279.1|CB978279
EST:     GTTTCGGCAGCATTTGAGCGACCAAAGGAATGAAAGGTTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|77588937|gb|DV223719.1|DV223719
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|71886760|gb|DT035815.1|DT035815
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|71889922|gb|DT038977.1|DT038977
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|27584894|gb|CB007589.1|CB007589
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
EST: gi|71886201|gb|DT035256.1|DT035256
EST:     GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCTGGAG                         TGACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT
genomic: GTTTCGGCAGCATTTGGGCGACCAAAGGAATGAAAGATTTCCCTCCGGAGgtaattttgg ... gcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgttttgctttgttgaaaaacccctgataggaagatgatgtagcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGTTAGCAACAGCTGGTGGGAACCATGATTCTGGAAACAGGCCACTTATGTA
                        ccctgat  putative branch site (score: 4)
               ttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttggttgccacccatattagttcatttgtttttccctgttttgctttgttgaaaaacccctgataggaagatgatgtagcaagtgcagTAACCAGCGGAACATTAGATGCTATTAGGGAGAGGATGAAGAGCATCCAGTTAGCAACAGCTGGTGGGAACCATGATTCTGGAAACAGGCCACTTATGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG