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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacacattcttataattcttcatctttcagatagatttcaagagattctaaaatgtttctgtttctcccttatgaacag

Basic information

species Vitis vinifera
transcript Vv19s0090g00560.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 5'ss of exon 9
CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaaga----cacattcttataattcttc---------atctttcagatagatttcaagagattctaaaatgtttctgtttct-----cccttatgaacag
||||||| |||   | |||| | |  ||    |  || || ||  | || |||||||||||||||||||||||||| ||| || | |||||||     |||||  || ||| | |||         || | ||   |   ||||    |     ||||| |      || |     ||||| |   |||
CAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcatcacatggttttaactgttctttctgacaatgtctcctttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccag

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G132866_T02 (Zea mays), 5'ss of exon 7
CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagac-acattcttataattcttca----tctttcagatag--attt---caagagattctaaaatgtttctgtttctcccttatgaacag
|||| || |||   | | |  |||  ||    |  || || ||  | ||||| |||||||||||||||||||||||  || |  |||||||||   |  || |    |   | ||    ||||   |||||  ||||     | || |  | | |  | | |||   |||||      |||
CAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAAgtaagcttatcttgtgggcagagtccaggtctcttgaggatagtaattttgctgaaagttgttgacacatgtttgtgcttccctccactccag

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT4G26940.1 (Arabidopsis thaliana), 5'ss of exon 8
CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaaga----cacattcttataattcttcatctttcagatagatttcaagagattctaaaatgtttctgtttctcccttatgaacag------
| || || ||||||   ||||| ||  ||||    || ||  |  | |||||||| ||||||||||||||||||||||| ||||| |||||||     ||| ||| |  ||     ||    |||      |||  |  | || |   |  ||  | | ||||    ||   ||       
CCACGCTTGGAGCAGAATTAGCAAGATACCGGATGAAGCCCCGAGTGTACATTGGTTGCATGAAATCTGGACCTGTTCTTGCTCAGAAgtaagttgttcaccttccttcaagagaccactcctca------tttttaatgtttgtctcactttcatctctctctgaaatttccaattttag

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT4G26940.2 (Arabidopsis thaliana), 5'ss of exon 8
CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaaga----cacattcttataattcttcatctttcaga--tagatttcaagagattctaaaatgtttctg---tttctcccttatgaacag---------------------------------------------------------------------
| || || ||||||   ||||| ||  ||||    || ||  |  | |||||||| ||||||||||||||||||||||| ||||| |||||||     ||| ||| |  ||     ||    |||    ||   ||      | | | |  | | ||||   ||||    ||  ||  ||                                                                     
CCACGCTTGGAGCAGAATTAGCAAGATACCGGATGAAGCCCCGAGTGTACATTGGTTGCATGAAATCTGGACCTGTTCTTGCTCAGAAgtaagttgttcaccttccttcaagagaccactcctcatttttaatgtttgtctcactttcatctctctctgaaatttccaattttagaggagtgagatatcatgaacccgaatactggaaatttggagaagagggtaacaaatacttccgccatgccacag

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|34544134|gb|CF512366.1|CF512366
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGGATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|349826233|gb|FQ416038.1|FQ416038
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|71875910|gb|DT024965.1|DT024965
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|77583730|gb|DV220900.1|DV220900
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|34544220|gb|CF512452.1|CF512452
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGGATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|71875911|gb|DT024966.1|DT024966
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|110385919|gb|EC950479.1|EC950479
EST:     CATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|351046999|gb|FQ454609.1|FQ454609
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|110712361|gb|EE089898.1|EE089898
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
EST: gi|351056608|gb|FQ442436.1|FQ442436
EST:     CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA                         GGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA
genomic: CCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacaca ... ttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAAgtaagacacattcttataattcttcatctttcagatagatttcaagagattctaaaatgtttctgtttctcccttatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA