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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagagttgagtttggtagtcgagctgagctgagggttggttttgtttaggaacattcatctccatgttgcagaattttaacactaccaaacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAGGCAAGTTTTTGAGCCATTCTAGACGAAATCACCTTCAAGACTGATTACA

Basic information

species Vitis vinifera
transcript Vv09s0018g01780.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G120579_T03 (Zea mays), 3'ss of exon 3
--aacagagttgagtttggtagt-cgagctgagctgagggttggttttgtttaggaacattcatctccatgttgcagaattttaacactaccaaacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAGGCAAGTTTTTGAGCCATTCTA-GACGAAATCACCTTCAAGACTGATTACA
  |   | |  | |     |  |      |   ||        | ||    ||| |       ||    ||| ||   ||| | |     |  |  |   ||||||||| ||||||| || || |||||||||||||| ||  |||||||||| || || || |   |   |  | ||  |     ||| | |   |  |||  
gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatagaactcgatgtcattttgt-gccacattctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT-
















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|29784297|gb|CB344831.2|CB344831
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110375956|gb|EC940987.1|EC940987
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110386695|gb|EC951311.1|EC951311
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110411796|gb|EC977519.1|EC977519
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|111125066|gb|EE253677.1|EE253677
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGCTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110372559|gb|EC936737.1|EC936737
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110387079|gb|EC951719.1|EC951719
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|29784413|gb|CB345109.2|CB345109
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTTTCCAACAG                         GTTCTTGGTAATAGTTTGCGGTATTTCTTGAGGGGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110385943|gb|EC950505.1|EC950505
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110413183|gb|EC978960.1|EC978960
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|110372429|gb|EC936593.1|EC936593
EST:     AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
EST: gi|29785638|gb|CB342854.2|CB342854
EST:     AGTTTCGTGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAG                         GTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG
genomic: AGTTTCATGTCAGCTACCGCGGAAAAGCCATCATCAAGCCTCTCCAACAGgtaaaattag ... aacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaggaacattcatctccatgttgcagaattttaacactaccaaacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAGGCAAGTTTTTGAGCCATTCTAGACGAAATCACCTTCAAGACTGATTACA
                               ttttaac  putative branch site (score: 2)
                           agaattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagagttgagtttggtagtcgagctgagctgagggttggttttgtttaggaacattcatctccatgttgcagaattttaacactaccaaacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAGGCAAGTTTTTGAGCCATTCTAGACGAAATCACCTTCAAGACTGATTACA

aacagag
- - - - - - - - - - - - - - - - - gggttgg
- - - - - - - - - - - - - - - - - - - - - - - - -aggaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactacc