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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatggatgtgctatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG

Basic information

species Vitis vinifera
transcript Vv03s0038g03120.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 2
------atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatggatgtgctatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
      || |  |  ||        |  ||||| || |   |||   ||| |  |  |   |     ||||   | |    |   | | | || | ||||| | |||| || || ||||||||||| ||||||||||| || || || || |||||||| |||||||||||||||||||| ||||
tgaaggatgttttcttgattgtcacagagtttt-caga---tcaagtttgtttgattaactaggaacttttgatttagcatgctcttgttttg-tgtgttt-gtagGTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 2
atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaatta--ttttctgtcaattggtgatgga------tgtgctatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
      ||||       |  |  |   | ||||  | |   ||  || ||   |  |||||  ||  ||||  | |    |   |      | || |   ||||| |||| || || ||||||||||| ||||||||||| |||   || || |||||||| |||||||||||||||||||| ||||
------ttctaaagggctttttttccagaataatatgaagatt--tcaaatgatttaattagattacctgtggagtttgaacatacttttctttggttccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatgg-atgtgc-tatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
                                            ||  ||           |||||  ||    | |||      |  |    |      | | |  || | |   |||||| |    ||||  | | |    ||||| ||||| ||| | |||||||  |||||||| ||||||||||||||||||||||| || ||||| |||||||| ||||
gtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccagGTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAG

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 2
atatgcttctggccaattaatggtttt-gcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatggatgtgctatg--ttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
 | ||||| |   || |    ||||||   |   |||   |   | |      ||  |    |||  ||   ||| |  | ||  ||| ||||  |||||||||| ||||| ||| | || |||| | |||| || ||||| ||||||||||||||||| || |||||||||||||||||||
ctctgcttttttacattgttcggttttcataaggcttggaaaacgatatttagctgca--cgtttggtgagtatttg-aaagggcgtggtatgatttttgcagGTAACACCAAATTTGTACGGAACTTTGGTAGCCAATACCGCAGCTGGTATTGCAGGCGGAACTGGTGTCATGCCAGGAG

upper sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 3
atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatggatgtgctatg--ttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
 |    ||  |     ||  |  | ||||||||  | || |       ||          || |  ||   | | |  |||| |||  ||||  |||  ||||| ||||| ||| | || ||||   |||| || ||||| ||||| ||||||||||| ||||||||||||||||||||||
-ttcaatttagttttttttcttatgttgcataaaattagggaaatgataatcagctgtacatatggtgcgtacttg-aatgggtgttgtatggatttctcagGTAACACCAAATTTGTACGGAACCTTGGTAGCTAATACCGCAGCCGGTATTGCAGGCGGCACTGGTGTCATGCCAGGAG

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|110356554|gb|EC919465.1|EC919465
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|110685778|gb|EE062796.1|EE062796
EST:     TGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATCGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: TGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|351048104|gb|FQ442074.1|FQ442074
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCACCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|161713512|gb|FC063119.1|FC063119
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|110388854|gb|EC953649.1|EC953649
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|71888504|gb|DT037559.1|DT037559
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|110369366|gb|EC933524.1|EC933524
EST:     ATAACTGCTGCATGCAACTGGTTTCNAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|110385879|gb|EC950436.1|EC950436
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|110419530|gb|EC985766.1|EC985766
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|161714849|gb|FC063000.1|FC063000
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
EST: gi|161708773|gb|FC060065.1|FC060065
EST:     ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATG                         GTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT
genomic: ATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggct ... tgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacactaaaattattttctgtcaattggtgatggatgtgctatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG
     cactaaa  putative branch site (score: 2)
        taaaattattttctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgcttctggccaattaatggttttgcataacttcagagttggtccaacactaaaattattttctgtcaattggtgatggatgtgctatgttttgcagGTGACACCTAATCTTTATGGAAATCTGGTGGCAAATACTGCAGCTGGTATTGCAGGAGGCACTGGTGTCATGCCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - ctggcca
- - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - gagttgg
- - - - - - - - - - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtg