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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT

Basic information

species Vitis vinifera
transcript Vv18s0041g00730.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G26600.1 (Glycine max), 3'ss of exon 1
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT----------------
    | |||   ||| ||  |   |   |  |   | |  |  ||   |  |  |  | ||   | | |||||||      || | || | ||| ||      || ||   ||   |  ||   ||||  |||     |||||| |||| ||||| ||| |||| ||||| ||||||||||||||||||||||| |||||                
----cccattagaggctaaaatagattgtggtctatatggtggttaactggttaagtttctgtttgctgaatttgc-----tactttgtc-tctctgtt----atgttttatagGCTAGTCTTCCTGT--TATCACAAACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT

upper sequence: Vv18s0041g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G28310.1 (Glycine max), 3'ss of exon 1
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttat--attctgccatc-tttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT-------------------
        ||| |  |||||    |    ||||     |  ||||   | ||||   ||   ||||   |  ||   |||    | | |||   | ||||   ||| || |     ||||  ||||    | | |      |||||||||||||||   ||| | || ||||||||||||||||||||||||||||| |||||                   
-------ttattaaaatatttgtga----ttttgtaagtgcttttgagtgatgg--ttaactgattgtcaccttccatttgctaaatttgcttccatttggttgcatttgtagGCTATTTTTTCAGCTATTGCCA------ACAATGGCTGATGGT---GAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAGAGCATTGGAATCTGCA

upper sequence: Vv18s0041g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G07560.2 (Glycine max), 3'ss of exon 1
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT----------------
     ||| |||| ||| | ||   |||||    | |  | |   | |  ||  |  |  | |  | |    || ||||  | || |||    ||||       | |    || | | |        || |||     |||||| ||||  |||| ||| | || ||||||||||||||||||||||||||||| |||||                
-----tca-atcacgat-tcaatacccattagaggctaaaatagattaagatctatatggtgg-ctaactggttaagttgctgtt-tgctgaatttgttatgtttatagGCTAGTCTTCC-------TATTATCACAAACAATGTCTGACAGTCAAGAATCTGACAAGAACATTGAGATATGGAAGATCAAGAAATTGATCAAGGCTCTGGAAGCT

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|349829600|gb|FQ421118.1|FQ421118
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|351012628|gb|FQ430191.1|FQ430191
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|110730728|gb|EE108140.1|EE108140
EST:     CTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTATC-ATATTGCACAATGGCTGAT
genomic: CTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTA-CTATATTGCACAATGGCTGAT
EST: gi|110690380|gb|EE067430.1|EE067430
EST:     ATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACCATATTGCACAATGGCTGATG
genomic: ATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|349830032|gb|FQ420292.1|FQ420292
EST:     GTTCTCTTTCTCTCTCTACGCCGCTCTTCGATCTATGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|351013136|gb|FQ424841.1|FQ424841
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|161714751|gb|FC063923.1|FC063923
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|351018783|gb|FQ425685.1|FQ425685
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG
EST: gi|294963803|gb|GW836653.1|GW836653
EST:     GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTG                         GCAATTTTCATTAATTTCCTCAGTCCGTACCATATTGCACAATGGCTGATG
genomic: GTTCTCTTTCTCTCTCTACGCTGCTCTTCGATCTAGGGTTTGgtaagttgct ... atctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT
                                           ccatcttt  CT-rich tract
                        aatttgagtttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-cacctca
- - - - - - - - - - -agcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgcc