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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcctccctttgccctatctgaaatcccaagccttccaatcatccatttaactgacatgtgaacatgtgcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCCGTAAGTGAATTTCCAGCATTGGACATAACGGCATTGAACAAGTTTTTGC

Basic information

species Oryza sativa
transcript LOC_Os07g26610.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 16
gtcagcctccctttgccctatctgaaatcccaagccttccaatcatccatttaactgacatgtgaacatgtgcatgc-acagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCCGTAAGTGAATTTCCAGCATTGGACATAACGGCATTGAACAAGTTTTTGC
    |     || | | ||  ||    || ||| |||    |  |  |||||    | |||||||   || |||||| |||||| | ||| || |||||||| |||||||| |||||||| || ||| |||| || | ||||||||||||| ||||  | |||||| ||||||| ||  |||
----gtagttctcttcacttcctc---tctcaatcctaatga--aggcatttcggagtcatgtga-tgtgcgcatgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCTGTGAATGAATTTCCAGCACTGGATGTGACGGCACTGAACAAATTCGTGC
















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|89183519|gb|CI046084.1|CI046084
EST:     TCTTATTGCGGTTATCCCTCCATGACGCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86869806|gb|CI316534.1|CI316534
EST:     TCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGC
genomic: TCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAA-GGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGC
EST: gi|86831683|gb|CI301533.1|CI301533
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86259591|gb|CI065464.1|CI065464
EST:     TCTTATTGCGTTTATCCCTCCATGACCCAGTTCTTCCCCTNAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|218504169|gb|FG954519.1|FG954519
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88268519|gb|CI378454.1|CI378454
EST:     TCTTATTGCGGTTATCCCTCCATGACCCACTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88262692|gb|CI366466.1|CI366466
EST:     TCTTAGTGCGGTTATCCCTCCA-GACCCAGTTCTTCCCCTTAACATCGAG                         TCGCCGAGCAAGGATGATGCCATTAATCTTGGGCTTGCAGTGCTGACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|89177577|gb|CI390756.1|CI390756
EST:     GCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: GCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88463145|gb|CI524455.1|CI524455
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86594297|gb|CI251169.1|CI251169
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86844097|gb|CI336754.1|CI336754
EST:     TCTTATTGCGGTTATCCCTCCATGACCCACTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTT-GGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|87008287|gb|CI301045.1|CI301045
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|29660679|gb|CB656954.1|CB656954
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88250179|gb|CI250456.1|CI250456
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|89186475|gb|CI048147.1|CI048147
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86426061|gb|CI071158.1|CI071158
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTGAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88838627|gb|CI376165.1|CI376165
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88845405|gb|CI084330.1|CI084330
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTGAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88828531|gb|CI073401.1|CI073401
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTGAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|88254849|gb|CI351477.1|CI351477
EST:     TTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTT-CAGTGCTTACTGCC
genomic: TTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86892585|gb|CI312008.1|CI312008
EST:     TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|89172967|gb|CI040860.1|CI040860
EST:     TATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG                         GCGCCGAGCAAGGATGATGCCCTTAAGCTTGGGCTTGCAGTGCTTACTGCC
genomic: TATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCC
EST: gi|86258642|gb|CI064995.1|CI064995
EST:     CTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCT-ANACATCGAG                         GCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGC
genomic: CTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTA-ACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGC

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: 74 (upstream exon), 66 (downstream exon)
Score: 26

GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctcc ... gcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCCGTAAGTGAATTTCCAGCATTGGACATAACGGCATTGAACAAGTTTTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccaagccttccaatcatccatttaactgacatgtgaacatgtgcatgcacagGCGCCGAGCAAGGATGATGCCATTAAGCTTGGGCTTGCAGTGCTTACTGCCGTAAGTGAATTTCCAGCATTGGACATAACGGCATTGAACAAGTTTTTGC
                          aactgac  putative branch site (score: 26)
                      atttaact  TA-rich tract