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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA

Basic information

species Oryza sativa
transcript LOC_Os09g38320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G451178_T01 (Zea mays), 3'ss of exon 1
----gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
    |  |  ||   |||| |      |   |        |     |||    ||   || || ||      |   |  |||| ||||      | ||||||| ||||| ||| ||||||| || ||||||||  | ||||| || ||||||||||||||||| ||| |||||||||||  |||||||||||| || ||| | ||||
aggcgccaccaagctcaaccaggagagccgaaggccggtgagacacacaacgctagccattttcag--aacccggtcagatgagtgact-----gctgttgtttcagGTGTGGTCTTCTCTTCTCCTGTACCGGTAGATCCTCGATGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACGTTCCGAAGACGAAGA

upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G475673_T01 (Zea mays), 3'ss of exon 1
gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA------------------------------
                                    |     |||    ||    | || ||      |   |  |||| ||||      | || |||| ||||| ||| |||||||||| ||||||||  | ||||| |||||||||||||||||||| ||| |||||||||||  |||||||||||| || ||| | ||||                              
---------------------------------gtgagacacacaacgctagccgttttcag--aacccggtcagatgagtgact-----gctgctgttacaggtgtggtcttctctactcctgtaccggtagATCCTCGACGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACGTTCCTAAGACGAAGAAGCTGATGGCGCTGCCCAAGGCGTACCTGA

upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G091887_T01 (Zea mays), 3'ss of exon 1
gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
                                    |     |||    ||    | || ||      |   |  |||| ||||      | || | || ||||| ||| ||||||| || |||||||| || ||||| |||||||||||||||||||| ||| |||||||||||  |||||||||| | || ||| | ||||
---------------------------------gtgagacacacaacgctagccgttttcag--aacccggtcagatgagtgact-----gctgctattacagGTGTGGTCTTCTCTGCTCCTGTACCGGCAGATCCTCGACGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACATTCCTAAGACGAAGA

upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G801291_T01 (Zea mays), 3'ss of exon 1
gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
                                    |     |||    ||    | || ||      |   |  |||| ||||      |||| |||| ||||| ||| ||||||| || |||||||| || ||||| |||||||||||||||||||| ||| |||||||||||  |||||||||||| || ||| | ||||
---------------------------------gtgagacacacaacgctagccgttttcag--aacccggtcagatgagtgact-----gttgctgttacagGTGTGGTCTTCTCTGCTCCTGTACCGGCAGATCCTCGACGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACGTTCCTAAGACGAAGA

upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC211183.3_FGT007 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------------------gtgagaaatgacaacta-catatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattag--gttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
                                                                                         | |  |   | || | | |  | ||   | |   |    | |   |  |  |   | | ||      |||| |     |   ||  | |    | || |||| ||||| ||| ||||||| || |||||||| || ||||| |||||||||||||||||||| ||| |||||||||||  |||||||||||| || ||| | ||||
gtatgtgccatgaggaagttgttcttctccgagtcggcctacaaggagaccaagctccacaccacgccccactcatggctgcccctcgagaggaaggcgccaccgagctcaaccaggagagcctatgaccggtgagacaca-caacgctagccgttttcagaacccggtcagatgagtgactgctgctgttacagGTGTGGTCTTCTCTGCTCCTGTACCGGCAGATCCTCGACGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACGTTCCTAAGACGAAGA

upper sequence: LOC_Os09g38320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G300238_T01 (Zea mays), 3'ss of exon 2
gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
                                    |     |||    ||    | || ||      |   |  |||| ||||      | || |||| ||||| ||| ||||||| || |||||||| || ||||| |||||||||||||||||||| ||| |||||||||||  |||||||||||| || ||| | ||||
---------------------------------gtgagacacacaacgctagccgttttcag--aacccggtcagatgagtgact-----gctgctgttacagGTATGGTCTTCTCTGCTCCTGTACCGGCAGATCCTCGACGAGATCGAGGCCAACGACTACGACAACTTCACCCGGAGGGCCTACGTTCCTAAGACGAAGA

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|33684314|gb|CF312553.1|CF312553
EST:     ACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: ACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGA-GCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|33676850|gb|CF305089.1|CF305089
EST:     AGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: AGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|33684315|gb|CF312554.1|CF312554
EST:     GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|88536824|gb|CI464614.1|CI464614
EST:     GGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTNACGAGATCGAGGCC
genomic: GGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|58690693|gb|CK079380.1|CK079380
EST:     GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|86508035|gb|CI150668.1|CI150668
EST:     GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|86538203|gb|CI178409.1|CI178409
EST:     GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGATCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACTAATCCTTGACGAGATCGAGGCC
genomic: GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
EST: gi|86538185|gb|CI178391.1|CI178391
EST:     GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCG                         GTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC
genomic: GACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCC

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: 51 (upstream exon), 56 (downstream exon)
Score: 9

ATGGAGATGTTTTATGAGGGATCAGATCACGAGAGCGAGGGCGTTTTTCAGACAGGCCGAAGAAGGCGCCAGCGAGCTCAATCAGGAGAGCCGATGGCCGgtgagaaatg ... gttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA
 tcttaat  putative branch site (score: 9)
     tatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaatgacaactacatatcctttaaaatttccatctgaacattcttaattatgttaagttggttcacacgtatgaatgaccattaggttgttgttgcagGTTTGGGCTTCTCTACTTCTGTACCGACAAATCCTTGACGAGATCGAGGCCAACGATTACAACAACTTCACCAAGAGGGCCTACGTCCCAAAGGCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG