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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA

Basic information

species Vitis vinifera
transcript Vv16s0022g00660.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g30160.1 (Oryza sativa), 3'ss of exon 4
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcattt-agGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA-
                   |||  |  | |||||| |||    |    | |||  | |     | |||| | |  |   |  |||  |  | | ||||  | |   |||   |        |  |||  |||| |||||| | |||||||   |||||||||  | ||||| |||||||| ||||| |||||||||||||| || ||  |  |      ||| | | || | |||  
-------------------gtgcata-tgttatttaaaaggtttcgacgtaat--cattgtgctgatat-aatagtaaattgatatgttatctgtcattctgat--actaactgtacctttttgtatcaattttagGTGTTTGATTTTGTTAAACTAACAGAATTGTACTATGCTGGTAGCCATGGAATGGACATCATGGGTCCAGTTGGGGAACATGATTC-AGTTACTAACCATA

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccattta-tatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactatt-catttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA
                                                             ||  | | | | | ||| ||  | | ||   |  | |||  || |   |||  |  |  |  | | || | ||||||| | | | ||||||   ||||  ||  | ||||||||||| || ||||| |||||||| ||||||||||| ||  |  | | |       |        
-----------------------------------------------------------gtatacagtgttattgttcattgcacaaataactcct-atcagcatt---ttgc-atttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
-----------gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatct-tcactgactt---gttacgtaac-ctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA
            |  || | |        |   | | ||||   |||  |||     |  | || |   | |   |  ||    |     ||   ||| | ||  |  ||  |  |||  |     || ||||   |  || ||   | |||| ||| | ||||| ||||||||||| || || ||||||||||||||||| ||||||||||| |||||||| ||||| ||  | ||| || | || | ||
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 4
gtaattggcaggctttt----------gagtgtgtgctattattttaaaatcattatggcaatttcctc-ccatttatatcagttttccttctatagatggtttttcatc-----ttca--ctgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA
||| |||      ||||          ||   | | ||||   |||  |||     |  | || |   | ||| ||    || |  | |||  | ||| | ||  |  ||      ||   || ||||   |  || ||  || ||   | |||| ||| | ||||| ||||||||||| ||||| || |||||||||||||| ||||||||||| || ||||| ||||| ||  | ||| || | || ||||
gtagttgaacaatttttataaaaaacagacaattttctatctctttttaattcccttatctatctgagcaccacttcatacactcctgctttca-agaagcttccttgtcggttgctcgttctaactttcgaattaccc--ctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTCTATTATGCTGGTAGTCATGGAATGGACATCATTGGGCCTGTTAGACAATCTGTATCTGATAATCACCCAA

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 4
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttcctt------ctatagat--ggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA
||| ||       |||  |         | | || |    ||  |||    | |  | |      ||| ||  |||||||      ||  || |  |  |||| || || ||    ||||||| || |||| |      | |||| ||| | ||||| |||||||  |||||||| || |||||||||||||| |||||||| || || |||   ||||| || | |||| || | || ||  
gtatttaaagaattttataaaacaaaacaattttctttc-tcggtatttttactcacacttgcacataacaaatttccttgttgatcttcagttttgacttttgattttaacc--tttgttacataccctattg---gctcagGTATATGAATTTGTTGGACTAAGTGAGCTCTATTATGCTGGTAGTCATGGAATGGACATTATTGGTCCTCCTAGACAATCTAATTCTGATAATCACCCTG

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S333_42V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------gtaattggcaggcttttg---agtgtgtgctattattt-taaaatcattatggcaatttcctcccattta------tatcagttttccttctatagatggtttttcatct----tcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA-
                                                     ||||||  | || ||   | |   | |  | |||   |  | | | |||  ||| |  | |  ||        | |||  |     |    ||| || | | |   |    || |||       |  |    |  | ||     |||||||  |||| |||  | || ||||  | || |||||||| |||||||| |||||||||||||| ||||  |    ||||  |  |  |     |  || 
gtactgacaggattcctggtattctgattctgtatcacactctgtccttgagcattggcttgtttctgttaaatccatacattgattcacatgaccttgatgcgaatattttgcagttggatgtagtgtcaaatcaaaattccgagagggatatgctgttgggatcgctgtgcctacagttggtatgtttttggagcagGTGTACGATTTCGTGCAATTATCAGAATTATATTACGCTGGGAGTCATGGTATGGACATCATGGGGCCTGCGAATGGCTCCGATGGTTTTCGT-GTGAAAG

upper sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA--
                ||  | | |  |   ||||||  ||||  || | | |||  |   ||  ||   |    | |   ||  |  ||     | |  |||| |  ||           |  | ||     |||||| | ||||||||  | | ||||| || || |||||||| |||||||| ||||| |||||||||||||  | |  |||   |  |  |  | |   ||  
----------------tggatctattttgagatttta--atcaggattg-attttggtgagatgcatgcgaaagcttcaatta--ggagg-----cgtgctcacagcttt---------tatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGT--TTCCGAGTTAAGG

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|30254979|gb|CB971426.1|CB971426
EST:     GAAGTCGGGATAAG                         GTATATAATTGANGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGG
genomic: GAAGTCGGGATAAGgtaattggca ... attcatttagGTGTATAATT-TTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGG
EST: gi|110365313|gb|EC928101.1|EC928101
EST:     TGGCTAAATTTTTCCCAACCGCAATAATTAGTGGAAGAAGTCGGGATAAG                         GTATATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGG
genomic: TGGCTAAGTTTTTCCCAACCGCAATAATTAGTGGAAGAAGTCGGGATAAGgtaattggca ... attcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA
                                              ttcattt  CT-rich tract
                                            tattcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA