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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttgctattgtttgatattctttcagtggtaagtggcaacacattttccactatgtgaaccacgagctgaattgtttgatgatatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGACCGGAATGTCACTGAGCAAACACTTAAGGCTATCTCTCTTATTACAAAGA

Basic information

species Oryza sativa
transcript LOC_Os07g19190.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G19410.2 (Glycine max), 3'ss of exon 1
-----------gtatttggttgctattgtttgatattctttcagtggtaagtggcaacacattttccactatgtgaaccacgagctgaattgtttgatgatatcaat-cagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGACCGGAATGTCACTGAGCAAACACTTAAGGCTATCTCTCTTATTACAAAGA
              |||| || |  || | | |   ||||  |   ||       |  ||  | |    |  | ||| |   |||   |||   |    ||     | |||||||| ||||||||||||||||| ||  | |||||||||||| | |||||| ||||| |  ||||| |    || ||||| ||  |    |||   || |
gtaaatcaattaactttgtttccctttctgtcagggtcttatacatgtgttgtttactactgtcttggtttggagaagcttcagcattattacatttacatgctgtttcagGACTCAACCTTTGAGTTTGAGAGAAAGCGAAACAGGCCAGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA
















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|29628204|gb|CB633215.1|CB633215
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|88372508|gb|CI610831.1|CI610831
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCG
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCG
EST: gi|86904503|gb|CI308713.1|CI308713
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|58688852|gb|CK077539.1|CK077539
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|58675839|gb|CK064526.1|CK064526
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|55412205|gb|CV724581.1|CV724581
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|218479728|gb|FG953387.1|FG953387
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAAAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|9865927|gb|AU101677.1|AU101677
EST:     TTAAATGGCCAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|58030381|gb|CX727924.1|CX727924
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|58591169|gb|CF989477.1|CF989477
EST:     TTAAGGGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|58589775|gb|CF988083.1|CF988083
EST:     TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAG                         GACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
genomic: TTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGAC
EST: gi|4881050|gb|AU065349.1|AU065349
EST:     TAAATGGACAAAAGCGTACAGGTGCTTNCATGGGGAAGGACATGACANAG                         G-CTTCACCTTTGAGTTTTAGGAGGAAAAGGACCAGGCCAGAGCG
genomic: TAAATGGACAAAAGCGTACAGGTGCTTGCATGGG-AAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAG-AGGAAAAGGAACAGGCCAGAGCG

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: 75 (upstream exon), 73 (downstream exon)
Score: 50

CCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGAAGGACATGACACAGgtatttggtt ... tatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGACCGGAATGTCACTGAGCAAACACTTAAGGCTATCTCTCTTATTACAAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacattttccactatgtgaaccacgagctgaattgtttgatgatatcaatcagGACTCCACCTTTGAGTTTGAGAGGAAAAGGAACAGGCCAGAGCGCTATGACCGGAATGTCACTGAGCAAACACTTAAGGCTATCTCTCTTATTACAAAGA
                                    gtttgat  putative branch site (score: 50)
                                aattgttt  TA-rich tract