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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g11960.3 (Oryza sativa), 3'ss of exon 3
catttataaggtttctctagttttgtgataatgtgaaa-actttttgattgattatagacttaaaagtttattcctt--caactctttccttcaaatttgt--agATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
            |||  | || |||  ||| ||| ||| |    ||  || ||  ||   || |  | | || | ||   || || |         |||||  |||||||| |||| ||||  ||||||||  ||||||||||||||||||| ||||||||| ||||||| || ||||| |
-----------gttccattgtcttgaaata-tgtaaaatatcagtttgttcatcttattgtttat-gctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG

upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 4
catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagac--ttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
            |||  |  | |||  |  ||||  | |   |   ||| ||| |   |   | | |   |||| || |  || | |           | |||||||||| |||||||  ||||||||||||||||||||||||||||| ||||||||||||||||| || || || |
-----------gttcggtcatcttg-aaggatgtatatataatcctattaattttgatcaactgataacctatttctgctgctttct-----------gaagATTTCATTGAGTGGGCCTCATTCCATTCTGGGAAGGGCAGTTGTTGTACATGCTGATCCTGATGACCTAGGGAGGG

upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
---------catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
         |||||    | | | | |   ||| ||| ||| ||||     ||| ||||  | ||||    | | || ||| | ||   |  |  |||  ||| |||||||| |  ||| |||    || |||||  | |||||||| ||||||||||||||||||||||||||||||||||| |
tattgttttcatttggttgatatttttg--tttatga-aatttgaatgtagtttaattgggtctaga----acacttaatttcctc--tttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG

upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G18100.2 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------cattta--taaggtttctctagttttgtgata-atgtgaaaactttttgattgattataga---cttaaaagtttattccttcaactc---tttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
                           || | |  ||| ||||  | |  |      || || |      | || ||||| | ||| |   ||   | ||||   | || | |||   ||  |||  ||||   ||||  |  | ||||||||| ||||||| || || ||||| |||||||||||||| ||||||||||| ||||| | ||
gtatatgatcttcttttttcacttcttcaatcatttaatgtttggcaaaataaacattacatttttcggttcttagattgttcatatatctctcggacgtttcaccatttatctcatcttgtctttgaattcacagATACCGCTTAGTGGGCAGTATTCCATACTCGGGAGGGCGGTTGTTGTGCATGCGGATCCTGATGACCTTGGGAAAG

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|349825158|gb|FQ415705.1|FQ415705
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|26263916|gb|CA814979.1|CA814979
EST:     GAGTTGCTGAGGTT-CAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|71870823|gb|DT019878.1|DT019878
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|110429247|gb|EC995737.1|EC995737
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|110392958|gb|EC957655.1|EC957655
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|32456166|gb|CD797340.1|CD797340
EST:     GAGTTGCTGAGGTTCCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|351040393|gb|FQ434526.1|FQ434526
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|71867553|gb|DT016608.1|DT016608
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|110389316|gb|EC954144.1|EC954144
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|110414987|gb|EC980855.1|EC980855
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
EST: gi|37184575|gb|CF603929.1|CF603929
EST:     GAGTTGCTGAGGTTTCAATTAAAGATATGCAG                         ATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT
genomic: GAGTTGCTGAGGTTTCAATTAAAGATATGCAGgtaatcagat ... aaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
 gattgat  putative branch site (score: 4)
                         ttccttcaactctttc  putative PPT
     attatagacttaaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - -tgaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttaaaa