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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaagggaattaaatttctgttacttgtaaatacatgtttatcagtgtatgtcatataaataggtatgcatatgcagactgacttgattttgctcatgatcctttacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTCTCTTGGAAGGAAGCAACAAAACCTTCTGTGCCTTCAACTGCAATGGCAG

Basic information

species Vitis vinifera
transcript Vv10s0003g00670.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g00670.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G014577_T01 (Zea mays), 3'ss of exon 15
---------------------------------------------------------------gtgaaagggaattaaatttctgttacttgtaaatacatgtttatcagtgtatgtcatataaataggtatgcatatgcag---ac-tgacttgattttgctcatgatcctttacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTCTCTTGGAAGGAAGCAACAAAACCTTCTGTGCCTTCAACTGCAATGGCAG-
                                                                | ||     | |||||  |   ||| | | || | |     ||  |  | | |  |  | ||    |||    |||||   || |    | | | |    |||||  ||      ||||||||||||||||||||| |||| |||||| || |||||||  |||   || || |||| ||| ||| |  ||         ||  || || | |  |||| 
gttccatcatcatagctcatcaccccctatcttcaatttgcccaactttcatatattacaggcctaaactactactaaatgacacataccttttaaaagagagccatatgatttttttgttgacattt-catgtgcttgcagtgtacatattctaactatatcaatgatgtttctt---tcagCCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCGCTCTATCATGGATGGA-GCATCCCAAG-----AAACCAACAGCTACGACAGCAGG
















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|30125073|gb|CB910412.1|CB910412
EST:     ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAG                         CCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC
genomic: ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAGgtgaaaggga ... tacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC
EST: gi|110362029|gb|EC925536.1|EC925536
EST:     ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAG                         CCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC
genomic: ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAGgtgaaaggga ... tacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC
EST: gi|110384203|gb|EC948624.1|EC948624
EST:     ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAG                         CCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC
genomic: ATACTACAACTGGTTTGAGAACCTGCAATAACATTCTGGCTATGACACAGgtgaaaggga ... tacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggtatgcatatgcagactgacttgattttgctcatgatcctttacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTCTCTTGGAAGGAAGCAACAAAACCTTCTGTGCCTTCAACTGCAATGGCAG
                                        tcctttac  CT-rich tract
                        ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaagggaattaaatttctgttacttgtaaatacatgtttatcagtgtatgtcatataaataggtatgcatatgcagactgacttgattttgctcatgatcctttacaactcagCCATTGCATTCAAAATCACCTTCATTTATTGGGGATAAGAGGATCAACCTCTCTTGGAAGGAAGCAACAAAACCTTCTGTGCCTTCAACTGCAATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA