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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttacacacatacattagaaaatgatatacctgccgcaagtcaatttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC

Basic information

species Vitis vinifera
transcript Vv18s0001g02810.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 11
---------------------------------------------------------------------atgtttaca-cacatacattagaaaatgatat-acctgccgcaagtca-atttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
                                                                        ||| |  || |   ||| |||  | |  | |      ||||  ||  |  | |||    |  ||   | | ||| |       |    ||  |  | ||||| || ||||| || || |||||||||||||||||||| |||||||||||  || |  ||||  ||||||| || ||  |||| || |||||||| || |
gtttgtattctccactcacctcgtccatcaataatgtagggtgcatccttggatgaactctagacctggccctttgcggcatactaatttgaacgtaagctgaaaatttgcaaaccacgtccacttttagaatgaaaaattcaactctaatgacataaacttgctatttcagGCTGCGAAGCAAGCGCGACTGGAGAAGTTTGAGATCCCGGCCAAGATCAAGCTGATATCTGAGCCATGGACCCCGGAGTCTGGCCTTGTCACTGCTGCCC

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 9
--atgtttacacacatacattagaaaatgatatacctgccgcaagtcaatttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
  ||   ||  | |||    |      |    |   |  |   ||    ||   || ||    |||||     | |||     |   |   |  || | ||||| |  ||||| |||||  ||||||||||||||||||||||||| |||||  || | || ||  | ||||| || ||  | || || ||||| || || |
taataggtat-cgcatgatgtgttgggtatggtttttttcttgagcacgttgtgttggtatgataattacttgattttactgatacatgcatgttctt-cagGCTGGTAAGCAAGCACGGTTGGAGAAGTTTGAGATCCCTGCCAAAATCAAGCTGATACCGGAGCCGTGGACGCCGGAGTCAGGCCTCGTCACGGCTGCCC

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 10
atgtttacacacatacattagaaaatgatatacctgccgcaagtcaatttaatttgttcactaattttgccactt--tttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
|  ||| | | | ||| ||   | ||     || |      |   ||| |  |      | |||  | |  |     ||| ||||| |      |  | |||| || | || |||| ||| ||||||| |||||||| ||||| || || ||||||||| ||||| |||||||||||||| |||| || |||||||| ||||
aaattttctctcttactttt--atatctctcacttaattgtataaaatgttgtaaaaaaaataaagtaggaataaaatttttctttatgcaaccttctgcagGAAGGACAGAAGGCTCGTTTGGAGAAATTTGAGATTCCTGCAAAAATTAAATTGCTTTCTGATCCATGGACTCCTGAATCTGGCCTAGTCACTGCTGCTC

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 10
atgtttacacacatacattagaaaatgatatacctgccgcaagtcaatttaatttgttcactaattttgccactttttctctttgtttttaatcat--acagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
|| || ||  |  ||||  | | |  | ||| | |  |     |   |  ||    | |  |||  ||      ||||||   | |  | || |||   |||| |||||||  ||| ||||||||||| |||||||| ||||| ||  | || |||||| ||||  |||||||||||||| |||| || |||||||||||||
attttaacgga-gtacaacatacatcg-tattcatagcctttattgttgcaacaaatgctgtaacattattctattttcttactatcgtaaaccatttccagGAAGCAAAGACGGCTCGTCTGGAGAAATTTGAGATTCCTGCAAAAGTTAAGTTGCTTTCTGAACCATGGACTCCTGAATCTGGCCTAGTCACTGCAGCTC

upper sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 13
atgtttacacacatacattagaaaatgatatacctgccgcaagt---caatttaatttgttcactaatt-ttgccactttttctctttgtttttaa---tcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
       ||||| |   |   |   | ||||  ||  |  || |    ||| |  | |    ||||||  ||   | |    || ||  || | ||   |  | |||| || |||| || | ||| |||| || |||||||| ||||| || || ||||||||| ||||| |||||||||||||| |||| || || ||||| ||||
-------cacacttctctcttacttttatatctctcacttaattgtataatatgttgtaaaaactaataattaggaataaaacttttctttatgaaatcttttgcagGAAGGAAAGAAGTCTCGTTTGGAAAAATTTGAGATTCCTGCAAAAATTAAATTGCTTTCTGATCCATGGACTCCTGAATCTGGCCTAGTTACTGCTGCTC

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|110385455|gb|EC949983.1|EC949983
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|110418478|gb|EC984635.1|EC984635
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|110389647|gb|EC954503.1|EC954503
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|110407339|gb|EC972939.1|EC972939
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|110364169|gb|EC923466.1|EC923466
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|27587007|gb|CB009702.1|CB009702
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
EST: gi|30330600|gb|CD013862.1|CD013862
EST:     TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAG                         GCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA
genomic: TATGCCAGAAAGAAGAAACTGTGAAGGAAGTACATGCATCACTTGTGAAGgtaggcctat ... aatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC
                   ttttgccactttttct  CT-rich tract
                                    tttgtttttaatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttacacacatacattagaaaatgatatacctgccgcaagtcaatttaatttgttcactaattttgccactttttctctttgtttttaatcatacagGCAGCAAAGCAGGCACGTCTGGAGAAGTTTGAGATCCCTGCCAAGATCAAATTGCTTCCTGATGCATGGACTCCTGAAACTGGGCTGGTCACTGCAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - acacaca
- - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - -acctgcc