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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtggagtatggtcataacgagaattgtcagaattggcaattattgcttcaagcaacaaaaggtcaattaatatttttcattatgggttgttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGGAGATCACTTATTGCTAACACTTGCTGCCTAGTTAATCGGGTCATTGGAG

Basic information

species Vitis vinifera
transcript Vv09s0070g00580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0070g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------tagtggagtatggtcataacgagaattgtcagaattggcaattattgc----ttcaag--caacaaaaggt-caattaatatttttcattatgggttgttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGGAGATCACTTATTGCTAACACTTGCTGCCTAGTTAATCGGGTCATTGGAG
                                             |   | |||     |||  |||    |    | |    ||| ||||    || ||      || | ||    |||  ||| | |     || | | ||  ||||||| || ||  | ||||| |||||||||||||  || |||||||||||||||||||| || || ||||||||||||||| | || ||| |||||| ||| |
gtgagctcaatatccatgttatatttccgattctcatcttcgtaggcacattatttatttaaatagatcacttcctactttggatttttgcactgttaaaatttggcatatggcgtgattcttatatgtgcccctgtgatttt-ttgtagGTGCGAGAATTAGTTCTGTCACGAGATCTTACACTCATCATTGAACCTGGGAGATCCCTCATAGCTAACACTTGCTGCTTCGTCAATAGGGTCACTGGTG

upper sequence: Vv09s0070g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G090722_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------tagtggagtatggtcataacgagaattgtcagaattg----gcaatta-ttgcttcaagcaacaaaaggtcaattaatatttttcattatgggt-tgttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGGAGATCACTTATTGCTAACACTTGCTGCCTAGTTAATCGGGTCATTGGAG
                                               |     | ||  | | ||    | || ||   ||||     |  | | ||   | | ||||  |  | |  ||| ||  |  |  || |   | | ||| || |||| || ||  | ||||| || | |||||||| |||||| ||||||||||| |||||  | |||||||| ||||||||| | || ||| | || | ||| |
gtaagctcagcattcttaccatgtttctgattcatatctttgcaggcacacatgcatctttaaaatagcagttctccttattgtgatacggtaagttagcttatgcaattatggcttgattcatcatggtggttctatttattttgttgcagGTACGAGAATTAGTTCTCTCTCAAGATCTTACTCTTATTATTGAACCTGGAAGATCCTTGATTGCTAATACTTGCTGCTTCGTCAATAGAGTAACTGGTG
















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|71871054|gb|DT020109.1|DT020109
EST:     CTCC-AGAGATCTTATAGATACA                         GTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
genomic: CTCCGAGAGATCTTATAGATACAgtgaggatca ... gttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
EST: gi|30130303|gb|CB915642.1|CB915642
EST:     ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACA                         GTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
genomic: ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACAgtgaggatca ... gttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
EST: gi|349825530|gb|FQ419447.1|FQ419447
EST:     ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACA                         GTTCGGGAGCTGGTTCTTTCACGAAATCTTAATCTTATCATTGAACCTGGG
genomic: ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACAgtgaggatca ... gttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
EST: gi|110416615|gb|EC982607.1|EC982607
EST:     ACTACCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACA                         GTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
genomic: ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACAgtgaggatca ... gttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
EST: gi|30256273|gb|CB972116.1|CB972116
EST:     ACTATCATGCTGGTGCTGTCCTTCCCACTCCAAGAGATCTTATAGATACA                         GTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG
genomic: ACTATCATGCTGGTGCTGTCCTTCCCACTCCGAGAGATCTTATAGATACAgtgaggatca ... gttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcaagcaacaaaaggtcaattaatatttttcattatgggttgttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGGAGATCACTTATTGCTAACACTTGCTGCCTAGTTAATCGGGTCATTGGAG
                     aattaat  putative branch site (score: 3)
             aaaaggtcaattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtggagtatggtcataacgagaattgtcagaattggcaattattgcttcaagcaacaaaaggtcaattaatatttttcattatgggttgttgctgtagGTTCGGGAGCTGGTTCTTTCACGAGATCTTAATCTTATCATTGAACCTGGGAGATCACTTATTGCTAACACTTGCTGCCTAGTTAATCGGGTCATTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - -aacgaga
- - - - - - - - - - - - - - - - - - - - - - -tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa