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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttataaaacaaatttcaaagatcattaaatttgtctttttgctttccttttcttttttctttatttaatcctttctgtgaatactgatgaaatattttgatttccctgactactgacatttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGATAAGTGATTGCTGCGTTGTATTAGGGAAG

Basic information

species Vitis vinifera
transcript Vv19s0090g01020.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G46300.1 (Glycine max), 3'ss of exon 5
gtatcctttataaaacaaatttcaaagatcattaaatttg-tctttttgctttccttttcttttttctttatttaatcctttctgtg-aatactgatgaaatattttgatttccctgactactgacatttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGATAAGTGATTGCTGCGTTGTATTAGGGAAG
||||  |||  | |||||  ||    |||| ||   |||| ||        || ||| | |  || | || || | | |  | || | | |||   |||  | ||||    | |   | ||     ||||  |||||||||| || |  | ||||||||||||||||  |||| ||||||| |||| ||||||||||| || ||  | || |||
gtataattttaataacaagatt----gatctttctttttgctcaaggcctctttcttctatgcttacctttttcatttcaatttgagtattaccactgactttttttccccttctgaattatgtgaatttggtagATATGATATAATAGTAGATGCAACAGATAATGCTCCTACCCGGTACTTGATCAGTGATTGCTGTGTGGTCCTTGGAAAG
















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|77581239|gb|DV219545.1|DV219545
EST:     GAACACAAAGAAGCTTTACGCGCATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
EST: gi|351044077|gb|FQ452750.1|FQ452750
EST:     GAACACAAAGAAGCTTTACGCACATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
EST: gi|349815971|gb|FQ403612.1|FQ403612
EST:     GAACACAAAGAAGCTTTACGCACATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
EST: gi|161721075|gb|FC070004.1|FC070004
EST:     GAACACAAAGAAGCTTTACGCGCATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTAATCGATGCAACAGATAATGTCCCTAGCCGGTACATGA
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTA-TCGATGCAACAGATAATGTCCCTAGCCGGTACATGA
EST: gi|349813558|gb|FQ413792.1|FQ413792
EST:     GAACACAAAGAAGCTTTACGCACATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
EST: gi|351013602|gb|FQ429743.1|FQ429743
EST:     GAACACAAAGAAGCTTTACGCACATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
EST: gi|351020215|gb|FQ445822.1|FQ445822
EST:     GAACACAAAGAAGCTTTACGCACATCCAACGCTTTGGAGATTTTGAGCAA                         ATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT
genomic: GAACACAAAGAAGCTTTATGCACATCCAACGCTTTGGAGATTTTGAGCAAgtatccttta ... catttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtgaatactgatgaaatattttgatttccctgactactgacatttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGATAAGTGATTGCTGCGTTGTATTAGGGAAG
 ttccctgac  putative branch site 
                                             catttctt  putative PPT
               atgaaatattttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttataaaacaaatttcaaagatcattaaatttgtctttttgctttccttttcttttttctttatttaatcctttctgtgaatactgatgaaatattttgatttccctgactactgacatttcttagATATGATCTAGTTATCGATGCAACAGATAATGTCCCTAGCCGGTACATGATAAGTGATTGCTGCGTTGTATTAGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC