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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttacccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA

Basic information

species Vitis vinifera
transcript Vv13s0019g03870.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g01240.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------ctttttacccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatca--tttgaagcttttc-ttcacctcttttggatatt-------gcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
                                                                               | | |  ||||| ||  |  ||   | || |  |  |  |  | || || | |  || |  |   || |||| |  | | ||| |||    | |       |||   ||||  || |||||||||||||| ||| | ||||||||| | ||||| || ||||||||  |||||||||||||||  ||||| || || || || ||||| 
gtatgttgatgtcttgcgttagaatccatgtttgcatctttgaaccattacacaataaccctttcctcatctaaattgatatctgaccagtcatgaaaata---ataacatgttcttgactatcttctcatggcattagatactaacctttccacttaactcatttattcacttgtgaatgcatttagGAACATTTGGTTTGAAGCTGCTACTTTGGTTGCTGTTCCTCCACCGGTAGAAATATCAACTGGAAGTGTTCTGAAGTCTGCTTTAGCTGGAGGTCTTGCT

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g01270.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------ctttttacccagtgatagagttattcacaatagttaatcaaacaactcct-aaggcaatcatttgaagcttttct--tcacctcttttggata-ttgcaaac------agGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
                                                                               | | |  ||||| ||  |   | | | || |  |  |    || || || | |||| | | |   | | ||||   | | ||| |||    | |||| ||       ||||  || |||||||||||||| ||| | ||||||||| | ||||| || || ||||| ||||| ||||||||||  ||||| || || || || ||||| 
gtatgttgatgtcttgcgttagaatccatgtttgcatctttgaaccattacacaaaccctttccttcatctaaatcgaatatctgaccagtcatgaaa--aataataacatgttcttggccatcttctcatggcattaaatactaacctttccacttaactcatttattcacttgcgaatgcatttagGAACATTTGGTTTGAAGCTGCTACTTTGGTTGCTGTTCCCCCACCGGTAGAGATATCAGCTGGGAGTGTTCTGAAGTCTGCTTTAGCTGGAGGTCTTGCT

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G003033_T01 (Zea mays), 3'ss of exon 2
--------------------------------------ctttttacccagtgatagagttattc-acaatagttaatcaaac-aact-cctaaggcaatcatttgaagcttttct--tcacctcttttggat---attgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
                                         ||  |     |  | ||| ||||  ||||  | |   |  |  |||  ||      || || ||  ||||| ||  | | ||  | |   |   | ||||  |||||  || ||||||||||| ||||| |||||||||||  | |||||| | ||||||||||| ||||||||| |||  ||||| || || || || ||||||
gtatgtctgatgtatcctgttagaagaaacctgcagttgaattggctttagggaatagtgattctgcaattatcaccaattctgactatctttcatgattatatggtgctttcctaattatcttctcttacttcaaatgcattcagGAACATTTGGTTTGAAGCAGCCACCGTTGTTGCTGTCCCCCCACCTATAGAAATATCTGCAGGAAGTGTTTTGAAGTCTGCTTTAGCTGGAGGTCTTGCA

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G146378_T01 (Zea mays), 3'ss of exon 2
---------------cttttt------acccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
               | | ||      | || ||||| || ||      |     || | |  |  |    |   | |   | |||   || ||||| | |   ||  | ||| ||  |||||  || ||||||||||| ||||| |||||||||||  | |||||| | ||||||||| | ||||||||| |||  ||||| || || || || ||||||
gtatgtctgatgtatcctgttagaagaaacctgtgattgaattggctttagggaatagtgactctgcaatcatcaccaat-tctgacaattatcttctctttacttacaaatt-cactcagGAACATTTGGTTTGAAGCAGCCACCGTTGTTGCTGTATCCCCACCTATAGAAATATCTACAGGAAGTGTTTTGAAGTCTGCTTTAGCTGGAGGTCTTGCA

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 3
ctttttacccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttg-gatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
   | |    | |     | | ||||    |    || ||   ||    ||||       ||  |   | ||    |  | | ||  | |  | |   ||||||||| |||||||||||||| || || ||||||||| ||||| |||| |||||  ||||||||||||| |||||||||||||||||||| |||||| | 
-ggtattttaatttcctcaatgattctacttccacaagcagttaatgattaagattcatcttctatattattgactatttttattatggttatactttcagGAGTATCTGGTTTGAAGCTGCGACAGTAGTTGCTGTTCCACCAGCTGTTGAAATTCCTGCTGGAAGTGTGCTGAGATCTGCATTGGCAGGTGGCCTTTCT

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G35730.1 (Glycine max), 3'ss of exon 3
-------ctttttacccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
          ||| | || ||||  |  |     ||  ||| ||| |   |  | |     | || |||     || || ||      || ||| |||  |   ||||||||| |||||||||||||| || || ||||||||| ||||| |||| |||||  |||||||||| ||||||||||||||||||||||| |||||| | 
ggtattttaatttcctcaatgattcaacttacaccagcagtcaatgattaagattcatcttctat-attaaggactattttta-----ttatggttat-actttcagGAGTATTTGGTTTGAAGCTGCGACAGTAGTTGCTGTTCCACCAGCTGTTGAAATTCCTGCTGGAAGCGTTCTGAGATCTGCATTGGCAGGTGGCCTTTCT

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 2
-----ctttttacccagtgata--gagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
       |||  |||| | ||   || ||  ||| |    | || |  | || |  |   |  ||      | | |  |     |   ||||   | |     | || |  || |||||||||||||| |||||||||||||||||||| |||||||   || ||||||||  |||||| | ||||||||| || || || ||||| 
cccttagtttctcccattcatgttgatttcctcaaacacttcaaacttataatttttgttgtcata--ccaatggtgattgatgctatttttacttgt-----atagTAACATCTGGTTTGAAGCTGCGACTGTTGTTGCTGTTGCACCCCCTGTGGCCTTACCTGCTGGAGATGTTCTAAAATCTGCATTAGCGGGAGGGCTTGCC

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|110421076|gb|EC987364.1|EC987364
EST:     CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAG                         GAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA
genomic: CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAGgtaatattaa ... ttgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA
EST: gi|161707924|gb|FC055680.1|FC055680
EST:     CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAG                         GAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCGCCTGTGGA
genomic: CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAGgtaatattaa ... ttgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA
EST: gi|161706499|gb|FC055020.1|FC055020
EST:     CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAG                         GAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCGCCTGTGGA
genomic: CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAGgtaatattaa ... ttgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA
EST: gi|161716608|gb|FC065554.1|FC065554
EST:     CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAG                         GAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCGCCTGTGGA
genomic: CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAGgtaatattaa ... ttgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA
EST: gi|110381337|gb|EC946664.1|EC946664
EST:     CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAG                         GAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCGCCTGTGGA
genomic: CGGAATTTTATGCTTCTGCTACCATCTGATCGACTTCAAGATGATCCCAGgtaatattaa ... ttgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA
          aatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttacccagtgatagagttattcacaatagttaatcaaacaactcctaaggcaatcatttgaagcttttcttcacctcttttggatattgcaaacagGAGTATATGGTTTGAAGCTGCCACTGTTGTTGCTGTTGCACCACCTGTGGAAATATCTGCTGGAAGTGTTCTGAGATCTGCATTGGCAGGGGGCCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - ttaccca
- - - - - - - - - - -tattcac
- - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - caactcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcaatca