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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaggagaagctattgtaaaacttgaatttgcttttcatttaatgttaatgataattattatcatcaatgttataataacatcatattttgttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCGGGAGGAGTTCATCTAGAGATGACAGGCCAAAATGTGACAGAGTGTATTG

Basic information

species Vitis vinifera
transcript Vv18s0001g06250.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G35370.1 (Glycine max), 3'ss of exon 4
ggaggagaagctattgtaaaacttgaatttgcttttcattta-atgtt-aatgataattattatcatc--aatgttataataacatcatattttgttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCGGGAGGAGTTCATCTAGAGATGACAGGCCAAAATGTGACAGAGTGTATTG
         || |  |||  | | || ||| ||||  |   | | ||| ||   | |  | |||  |   |||| | |||  | |     | ||  | |  ||||| ||||| |||||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||||||||| || || |||||||| ||||| ||||
--ttattgtgcaaacgtactagt-gagtttactttctaaaaatacgttcaacattcaaaagtatttttcgaatggt-taaccaaacatggtcttaattgtacagGCTGAAGTGAGAGCATTCTTTGATGTGCACGAGCAAGAAGGAAGCCACCCAGGAGGGGTTCATCTAGAGATGACGGGTCAGAATGTGACCGAGTGCATTG

upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G37080.1 (Glycine max), 3'ss of exon 4
ggaggagaagctattgtaaaacttgaatttgcttttcatttaatgttaatgataattattatca-tcaatgttataataacatcatattttgttgga-gcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCGGGAGGAGTTCATCTAGAGATGACAGGCCAAAATGTGACAGAGTGTATTG
  |    ||   ||    ||| | || ||| |||||     |||       | | |||  |  | |   ||  |   |||    | ||  | ||     ||||||||||| ||||||||||| ||||| || |||||||||||||||||||| ||||| ||||||||||||||||| || || |||||||| ||||| ||||
-taactaaacacatcacgaaagt-gagtttactttttcaaaaatacgttcaacatttaaaagtactttttgaaaggttaatcaaacatacttttaattacagGCCGAAGTGAGAGCATTCTTCGACGTACACGAGCAAGAAGGAAGCCACCCAGGAGGGGTTCATCTAGAGATGACGGGTCAGAATGTGACCGAGTGCATTG
















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|352768988|gb|FQ468179.1|FQ468179
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110422524|gb|EC988849.1|EC988849
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110701596|gb|EE079344.1|EE079344
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110386697|gb|EC951313.1|EC951313
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|33405630|gb|CF211257.1|CF211257
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110414480|gb|EC980313.1|EC980313
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|352765061|gb|FQ473709.1|FQ473709
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTTTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|33405540|gb|CF211167.1|CF211167
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|71882133|gb|DT031188.1|DT031188
EST:     CGATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110423267|gb|EC989609.1|EC989609
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110361679|gb|EC925171.1|EC925171
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|34544849|gb|CF513081.1|CF513081
EST:     CGATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110423681|gb|EC990032.1|EC990032
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110689789|gb|EE066321.1|EE066321
EST:     CGATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCAATCATG                         GCCGGAA-TAAGAGCATTCTTTGACGTGCATGAACAAGAAGGAAGC-ACCC
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCG-AAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCC
EST: gi|110368361|gb|EC932335.1|EC932335
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110388773|gb|EC953560.1|EC953560
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
EST: gi|110381435|gb|EC934450.1|EC934450
EST:     CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGG                         GCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG
genomic: CCATCAAGGCTCCCTGTGGTCTCAAAACTCGCCCCTTCGATGCCATCAGGgtatgataaa ... gttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgataattattatcatcaatgttataataacatcatattttgttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCGGGAGGAGTTCATCTAGAGATGACAGGCCAAAATGTGACAGAGTGTATTG
                            taataac  putative branch site (score: 1)
                                         ttttgtt  putative PPT
      ataattattatcatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaggagaagctattgtaaaacttgaatttgcttttcatttaatgttaatgataattattatcatcaatgttataataacatcatattttgttggagcagGCCGAAGTAAGAGCATTCTTTGACGTGCATGAGCAAGAAGGAAGCCACCCGGGAGGAGTTCATCTAGAGATGACAGGCCAAAATGTGACAGAGTGTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- aggagaa
- - - - - - - -gtaaaac
- - - - - - - - - - - - - - - - - - - - - - - -aatgataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaca