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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT

Basic information

species Vitis vinifera
transcript Vv07s0130g00170.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaat-atctgacaacttgaacaaaaaactttgt----tgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                                                                                           | |  |  |  |  ||| |    |  | | |   | |||| | |     | || ||   |   |||||     | |||||||||| ||||||||||| ||  | ||||| ||||| |||||||| ||||| |||||| | || |||||||| ||||| |||||||||||||| |||||
--------------------------------------------------------------------------------------gtaagtaattactttctagttctctctgtgatctactagacaaattagcaatggattttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 10
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctg-acaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                                                           |||||     ||| ||      ||||| |   | |  |||  |   || | |  ||| ||    ||   ||| | ||  |   ||| ||   |||  | |||||||| || ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||
---------------------------------------------------------tctcacacttatccaatt------tcaatgcagatta-tatcattaagtttataagttttttaagctttgtaatgtttgtgctctttgtacttgaaaact-gttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA04G38120.1 (Glycine max), 3'ss of exon 10
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcac-atctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                                                             |||       |||    |  | ||      |||       || | | |  |  ||| |     || ||||  | | |    ||| ||       | |  || |||||| ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||
------------------------------------------------------------aacacagat--agtcacacacttaaccaatttcaatgcagattatattattaagtttataagttttgtaaactttttaatgtttgtactct---ttgtactgtagGTTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACTTACAAGTTTCTCAACACCAT

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                                                                                              |    |   || ||||  ||||   ||   | |||      ||  |  ||           |      ||||||||| ||||||||||| ||| | ||||| ||||| ||||| || || ||||| || || |||||| | || ||||| |||||||||||||| || ||
----------------------------------------------------------------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaa------gatcatgtgtgtgtgttgtgtga--aaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ13811 (Selaginella moellendorffii), 3'ss of exon 10
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                                                                                              |    |   || ||||  ||||   ||   | |||      ||  |  ||           |      ||||||||| ||||||||||| ||| | ||||| ||||| ||||| || || |||||||| || |||||| | || ||||| |||||||||||||| || ||
----------------------------------------------------------------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaa------gatcatgtgtgtgtgttgtgtga--aaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCTCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

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|33401807|gb|CF207434.1|CF207434
EST:     CTGGTACTCTTGGATCCTTTCTTCACTCACAAGCTGTGTCTACATGTTTG                         GTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTG
genomic: CTGGTACTCTTGGATCCTTTCTTCACTCACAAGCTGTGTCTACATGTTTGgtaagccctt ... tttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTG
EST: gi|110722903|gb|EE099605.1|EE099605
EST:     CTGGTACTCTTGGATCCTTTCTTCACTCACAAGCTGTGTCTACATGTTTG                         GTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTG
genomic: CTGGTACTCTTGGATCCTTTCTTCACTCACAAGCTGTGTCTACATGTTTGgtaagccctt ... tttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT
                      atctgac  putative branch site (score: 3)
                                            ctttgtt  putative PPT
        ttttcgttataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG