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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatttccttctgcatgatgtggaccactgccattttaagtatgatattttctgattttgttaaatatattgctgaagccttgtcattttattctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG

Basic information

species Vitis vinifera
transcript Vv15s0021g02450.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 8
atgatttccttctgcatgatgtgga-ccactgccattttaagtatgatattttctgattttgttaaata------tattgctgaagcct-tgtcattttattctac-agGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
         ||    || || || |  || ||  |            |||     || |   ||| ||       ||  | | || | | || |||| | || | | ||||||||||||||||  ||||||| || ||||||||||||
---------tttcaaataatatgaaatcattggtaaaacgtagcaattatgccaggaatacattagatgctcagttagagttaaaacttgtgccattatgtttttctagGTTCCTCGCTTGGTAAGGATGCACTCCAATGAGATGGAG

upper sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 8
atgatttccttctgcatgatgtggaccactgccattttaagtatgatattttctgattttgttaaatatat---tgctgaagccttgtcattt-tat-tctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
     || |||   | | |  |||   |  |     |   |  |  || | |   || ||  ||      |   |     | || |||  |||  || | |  ||||||||||||||||  ||||||| |||||||||||||||
-----tttctttaactttagttggtggatagggccatagggggtactactattgaatattcataggagggtgcatatctgatccctgtggtttgcatgtttttagGTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAG

upper sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 8
atgatttccttctgcatgatgtgg-accactgc-cattttaa-gtatgatattttctgattttgt----taaatatattgctgaagccttgtcattttattc-tacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
   |||||  |  | | |||  ||   || | |   | |||  ||||   |||    |||| | |    | ||| | | |||||  ||||    | || | | | |||||||||||||||||||||||||||||| |||||||||||
---atttcacta-gtaagatcaggtgtcattccatgtcttattgtattgcattccgagattatatatagtgaatttgtggctgagtcctt----tcttgtgcatgcagGTTCCTCGCTTGGTTCGGATGCATTCTGATGAGATGGAG

upper sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 3
-----atgatttccttctgcatgatgtggaccactgccattttaagtatgatattttctgattttgttaaatatattgctgaagccttgtcattttattctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
     | |||    | |      ||||  |  | ||    ||  | |   | ||| |   ||| |  | ||| | | |||||| ||||     | |||    ||||||||||| |||||||||||||||||| |||||||||||
ctagtaagatcaggtgccatgccatgtctattattgta--ttgcattccaagattatactattatagtgaatttgtggctgaatcctttcttgtgtat---gcagGTTCCTCGTTTGGTTCGGATGCATTCTGATGAGATGGAG

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|71863690|gb|DT012745.1|DT012745
EST:     TTCGGAAGGGTGATTTTATAATCAATGTAAACACAGGCAAAAAGATAAAG                         GTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
genomic: TTCGGAAGGGTGATTTTATAATCAATGTAAACACAGGCAAAAAGATAAAGgtgagttgaa ... tattctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttctgattttgttaaatatattgctgaagccttgtcattttattctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG
     ttctgat  putative branch site (score: 3)
                                          ttttattct  putative PPT
     ttctgattttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatttccttctgcatgatgtggaccactgccattttaagtatgatattttctgattttgttaaatatattgctgaagccttgtcattttattctacagGTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - tccttct
- - - - - - -gcatgat
- - - - - - - - - - - - - cactgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagcc