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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctataaaaggataaatcatatttattattctgcaattctgcttactacaaactggtagaccatcttatatttccatgttttgatgatgtccttgtcgtag

Basic information

species Oryza sativa
transcript LOC_Os06g45710.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G41550.1 (Glycine max), 5'ss of exon 3
GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctataaaaggataaatcatatt-tattattctgcaattctgcttactacaaactggtagacc--atcttatatttccatgttttg--atgatgtccttgtcgtag
|| || |||||||||||||| || || ||||| |||||||||||||| ||  |  ||||| | ||||||||  |||| || |||  |  |||  |    ||| || | || || ||  ||||     ||  |    | ||   |   || || |  ||      | ||  ||  | || |  |   ||
GGACGTCCAAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCAAGGCTGTCTCAACTTCTTGGAATTGAGgtgtgccttctaagc-tgctccattttgttttgttttggcattccttccacccccttttcgtttgcttgattttctgcttattcactgtgtcattttctcttgattacag

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 2
GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctataaaaggataaatcatatttattattctgcaattctgcttactacaaactggtagaccatcttatatttccatgttttgatgatgtccttgtcgtag
|| |||||||||||||| || || ||||||||||| ||||||||||| ||  | |||||||| |||||||||||||| || || |             |     || |     |||||   | || |  |  | ||  || |  | |   | ||  ||   | || |  |||   |       
GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcctc---------ttcctcttctagacttgcaaggtttctgaacattagcttttaaaagaacac-tgttctca--ctctgtttgtgttaatag-----

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 5'ss of exon 2
GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctataaaaggataaatcatatttattattctgcaattctgcttactacaaactggta-gaccatcttatatttccatgttttgatgatgtccttgtcgtag
|| |||||||| ||||| || || |||||||||||||| |||||||| ||  |  ||||||| |||||||| ||||| || || |     |      |  || | | || || ||  ||||             |||| | ||   |  |  | ||  |||  ||  |  | | | | |  |||
GGGCGCCCAAAGGGTGTTACACCTAAGTACAGCTTGAAACCTCTTGTGCCAAGGCTGTCTGAACTTCTTGGAGTTGAGgtttgttt----attccctaatatttctgttgttttgttattcaaacctgatttggctggcatgaatgtact-cacttggatgacttttttgtttgcctttactag

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|58589338|gb|CF987646.1|CF987646
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|33658427|gb|CF281040.1|CF281040
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|58677408|gb|CK066095.1|CK066095
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|58668078|gb|CK056764.1|CK056764
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|88313529|gb|CI671652.1|CI671652
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAA
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAA
EST: gi|88327337|gb|CI645117.1|CI645117
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAA
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAA
EST: gi|88392654|gb|CI625476.1|CI625476
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGT
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGT
EST: gi|29675440|gb|CB671715.1|CB671715
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|88393098|gb|CI616582.1|CI616582
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|33677818|gb|CF306057.1|CF306057
EST:     ACAGCTTGTTTCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|33813054|gb|CF332417.1|CF332417
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|33688490|gb|CF316729.1|CF316729
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|58689757|gb|CK078444.1|CK078444
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCC
EST: gi|88332298|gb|CI656167.1|CI656167
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAG
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAG
EST: gi|86849751|gb|CI301639.1|CI301639
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCG
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCG
EST: gi|88325004|gb|CI645019.1|CI645019
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGG
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGG
EST: gi|88353244|gb|CI654510.1|CI654510
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTC
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTC
EST: gi|88338304|gb|CI655493.1|CI655493
EST:     ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT                         GTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCA
genomic: ACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 59 (upstream exon), 75 (downstream exon)
Score: 94

GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctata ... cttgtcgtagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCCACTTTACCAGATGGTGGTGTTCTGCTTCTAGAAAATGTTCGGTTCTACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGATgtatgctataaaaggataaatcatatttattattctgcaattctgcttactacaaactggtagaccatcttatatttccatgttttgatgatgtccttgtcgtag

- - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT