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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g00500.t01
intron # 11
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 11
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
gtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggc-tagtattgacaagtta-tgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG
                                                                    ||||   |   | ||  |  | ||| |  ||  ||||  |    |  | |  |||    |   | | | || | | ||| | | ||| || |  | ||||||||||||||||| || ||||| ||||| || || || |||||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||| ||||
------------------------------------------------------------------ctaata-gcaatctgcatatagtccatatccat--cactatttgc-acccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 15
----------------------gtaagctttatctttaattt---ctatacattcaccattcatgtcttttc----attcttgatt--aaagtagctgcaata-cagagattc-caagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggc-tagtattgacaagttatgc-tgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG
                       ||  ||  |  |  || |    |||| | ||    || | | | ||||     || |||  ||  | | | |  |   ||  ||  ||   || ||  | |||||  ||  ||||  |    |  | |  |||    |   | | | || | | ||| | | ||| ||    | || ||||||| |||||| || ||||| ||||| || || || |||||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||||||||
gttagtagtagagtttgtcaggatattctgaagatccaaatagcactatgcttttggtatactttttttttttaaaatactttgtttgagaattgtggtgctaatagcaatctgcatgtagtccatttccat--cactatttgc-acccactggttttgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 11
gtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggc-tagtattgacaagtta-tgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG
                                                                    ||||   | || | | ||  | |||||  ||  ||||  |    |  | |  |||    |   | | | || | | ||| | | ||| || |  | || ||||||| |||||| || ||||| ||||| || || || |||||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||||||||
------------------------------------------------------------------ctaatagcaatatgc-atgtagtccatttccat--cactatttgc-acccactggttttgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 3
----------------------gtaagctttatctttaattt---ctatacattcaccattcatgtctttt----cattcttgatt--aaagtagctgcaata-cagagat-tccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggc-tagtattgacaagttatgc-tgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG
                       ||  ||  |  |  || |    |||| | ||    || | | | | ||     || |||  ||  | | | |  |   ||  ||  || | || ||  | ||| |  ||  ||||  |    |  | |  |||    |   | | | || | | ||| | | ||| ||    | || ||||||| |||||| || ||||  ||||| || || || |||||| | || |||||||| || |||||||||||||| ||||| |||||  ||||||||||||
gttagtagtagagttcgtcagaatattctgaagatccaaatagcactatgcttttggtatacttttttcttaaaaaatactttgtttgagaattgtggtgctaatagcaatctgcatgtagtccatatccat--cactatttgc-acccactggtttcgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGTGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGCACCTGATTAAAG

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:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|71866164|gb|DT015219.1|DT015219
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|110360549|gb|EC923744.1|EC923744
EST:     ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|34542727|gb|CF510959.1|CF510959
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|22015490|gb|BQ800524.1|BQ800524
EST:     AAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: AAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|110421496|gb|EC987793.1|EC987793
EST:     ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|34416104|gb|CF414858.1|CF414858
EST:     GAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGGCAGG
genomic: GAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|45368189|gb|CK906548.1|CK906548
EST:     ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|110385601|gb|EC950143.1|EC950143
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|30124998|gb|CB910337.1|CB910337
EST:     ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|110366510|gb|EC930420.1|EC930420
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|34320121|gb|CF372875.1|CF372875
EST:     GGGAGTGTCTCAAACAGAAT                         GTGGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGGCAGG
genomic: GGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|110697624|gb|EE074785.1|EE074785
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
EST: gi|30255672|gb|CB971804.1|CB971804
EST:     ACAATCCAGCCAAAATTCCCGCCTTTTCGCGGGAGTGTCTCAAACAGAAT                         GTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG
genomic: ACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagcttta ... gctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG
                               tattgac  putative branch site (score: 2)
                                              ctgttcc  putative PPT
                            tagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA