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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgtgtcactgtgcttcaatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA

Basic information

species Vitis vinifera
transcript Vv16s0050g01850.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA16G29290.1 (Glycine max), 3'ss of exon 3
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgt-gtcactgtgcttc---aatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
   || |    | |  ||    |||||   |    |||||  |  |  |   | |    |||   |    ||||| |  |   |    | ||| || ||| ||| ||  |||||||||| |||||||| |||| |||||| |||||||||||||||||  |||| |||||||||   ||  |  | ||||| || ||||| |||
---ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataacactcacctttttat-tgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA

upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 11
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgt-gtcactgtgcttc---aatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
   || |    | |  ||    |||||   |    |||||  |  |  |   | |    |||   |    ||||| |      |    | ||| || ||| ||| ||  |||||||||| |||||||| |||| |||||| |||||||||||||||||  |||| |||||||||   ||  || | ||||| || ||||| |||
---ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataactctcacctttttat-tgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAATTTAGACTTCAAAGAGCTGGCA

upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 11
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgt-gtcactgtgcttcaatcag-acaaactaatggtctata---tgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
      |    | |  |||   |||||   |    ||| |  |  || |   | |    |||   |    ||  | ||     |   || ||   || ||| ||| ||  |||||||||| |||||||| |||| |||||| |||||||||||||||||  |||| ||||| |||   ||  |  | ||||| || ||||| |||
-----ttcaactgtgcaatatcaatattcaatgcttttcagttcaattattattgctcttgtaacttgtgcatcataactcttttacctttatattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCA

upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA16G29250.1 (Glycine max), 3'ss of exon 1
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgt-gtcactgtgcttc---aatca-gacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
      |    | |  ||    |||||   |    |||||  |  |  |   | |    |||   |    |||||  ||   || |   | |   || ||| ||| ||  ||| | |||| |||||||| |||| |||||| |||||||||||||||||  |||| |||||||||   ||  |  | ||||| || ||||| |||
-----ttcaactgttcaacatcaatatttaatgctttttagttcaactattattgctcttgtaactagtgaatcataactctcttacctttttattgttgagcagGATCTTGGGTTGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA

upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA10G37380.1 (Glycine max), 3'ss of exon 10
atctt--ctgtgttatca---aatcaaaatatcagaaatgttttaagtagataagcgtgtcactgtgcttcaatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
 ||||  |  | | ||     | |     |  | || | |||  |||    |     | | |   |   | ||| | |    ||  |  |    ||| ||| ||| || ||||||||||| |||||||  |||| |||||| ||||||||||| |||||||| || || ||||||   ||  || | |||||||| |||||| ||
-tcttagccatatcattgcacagtttggtttccggataggttgcaagccattgt---ttttaagatttgtaaatgatatct-ctgttaattgcgatgttgagcagGATCATGGTTGGTCTTCCATCTGCTGAGAACAGGGAAATGATCTTGAAAACTCTCCTAGCTAAGGAAAAATATGAACATATAGACTTTAATGAGCTTTCA

upper sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA20G30360.1 (Glycine max), 3'ss of exon 10
atcttctgtgttatcaaatcaaaatat------cagaaatgttttaagtagataagcgtgtcactgtgcttcaatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
    |  |   ||||||  || | | |      |||| | |||  |||    |     | | |   |  || ||| | |    ||  |  |    ||| ||| ||| || ||||||||||| |||||||  |||| |||||| ||||||||||| ||| |||| || || ||||||   ||  || | |||||||| |||||| ||
--tcttagccatatcaatgcacagtttggtttccagataggttgcaagctattgt---ttttaagatttttgaatgatatct-ctgttaattgcgatgttgagcagGATCATGGTTGGTCTTCCATCTGCTGAGAACAGGGAAATGATCTTGAAAACTATCCTAGCTAAGGAAAAATATGAAAATATAGACTTTAAAGAGCTTTCA

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|34547829|gb|CF516061.1|CF516061
EST:     AACAGGCCATTTGACCTTGACGAGGCAATCATTTGGCGGTTTGAGCGCAG                         AATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGAC
genomic: AACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgt ... tgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGAC
EST: gi|110715259|gb|EE093108.1|EE093108
EST:     AACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAG                         AATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGAC
genomic: AACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgt ... tgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGAC
EST: gi|294967133|gb|GW840008.1|GW840008
EST:     AACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAG                         AATTATGGTTGGTCTAACATCTGT
genomic: AACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgt ... tgatgaacagAATTATGGTTGGTCTACCATCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagcgtgtcactgtgcttcaatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
                              aactaat  putative branch site (score: 2)
                             aaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgtgtcactgtgcttcaatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- cttctgt
- - - - - - - -aaatcaa
- - - - - - - - - - - - -atcagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - actgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa