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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC

Basic information

species Vitis vinifera
transcript Vv13s0019g05390.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 4
cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcat--gctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC---
    ||  |  | |     | ||| |  |   |    ||  |     |    |  ||| ||||||     |     || | | |   |  | |   ||   ||||||||||||    ||||||||  | || || |||||||| | ||||||||| ||||||| ||| |||||||| |||||||| ||||| ||||| ||||   
---ttaggttgccacattcagcctctctatcct-ccatgcatagtgcactgttgcttctatatttgttgttaaaggctcattttcttttggtttgtattt-gcagGAATGGGAGGCTATTAATGACTTAAGGGCTGATATGGCTAGGCTTCAGCAGGGCATGAGTCATATGCAAAGAATGTTGGAAGCTTGTATGGACATGCAGC

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 4
cacata-catgtcaat---cccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC---
   |||  | |  |||   | |||  ||   |   ||| |  ||||| |    | ||  |    ||| |    |      || |   |   |         |  |||||||||||    || |||||| | ||||| |||||||| |  ||||||||||||||||  || ||||||||||||||||| ||||||||||||||||   
---atagtaggctaatgcactcaactcttcgatttatagtaagtttggggagtagcttatatgttatgtgt-ggcaaaggctca---tatttttcttttctgtccagGAATGGGAGGCTATCAATGATTTAAGAGCTGATATGGCTAGACTTCAGCAAGGCATGAGCCATATGCAAAGGATGTTGGAAGCTTGCATGGATATGCAGC

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC---
    |  ||  |             ||    | || || ||  | ||  | || | | || |||        ||  ||   | ||  ||||||   ||| ||||| ||||| || || |||||| | ||| |||| |||||||  |||||||||||||||||||||||||| |||||||||||||| |||||||||||||   
--tttttattcctggagttttttctttgcctaaatagttttcatactgtatct-tattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 6
cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacc-tatttcaatatttcccagtttgaa---cttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC---
        | | | |||   |  | ||        |   |   |   | ||  ||||| | ||     |  ||||||   ||  || ||  ||||||   ||| ||||| ||||| || || |||||| | ||| |||| |||||||  |||||||||||||||||||||||||| |||||||||||||| |||||||||||||   
-------gttttattcctggagttttttctttgcctaaatagttttcatactgtattttattaaaattctttttgaagttctgggtttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC

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|33404834|gb|CF210461.1|CF210461
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|110362870|gb|EC926428.1|EC926428
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|110402602|gb|EC960544.1|EC960544
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         ---GAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|30302439|gb|CB979233.1|CB979233
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|110697361|gb|EE074284.1|EE074284
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|110722021|gb|EE097887.1|EE097887
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|33404749|gb|CF210376.1|CF210376
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|110396940|gb|EC962647.1|EC962647
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
EST: gi|30136916|gb|CB922254.1|CB922254
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         --G-AATNGGAAATGATTAATGATCTGAGAGC
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGC
EST: gi|34362695|gb|CF404280.1|CF404280
EST:     ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATT                         ---GAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG
genomic: ATTTACATCACACAAATTGGCCTCGTCACAGCATGCATCGTTCAGAAATTgtgagccatc ... tgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC
                                          tgctgac  putative branch site (score: 2)
       tatttcaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - -acatgtc
- - - - - - - - ccaaacc
- - - - - - - - - - - - - -aaagata
- - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc