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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttcctattttccatcaaatatccattctattggattatttttttatacttgtgtaatattttattttatggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG

Basic information

species Oryza sativa
transcript LOC_Os06g14740.1
intron # 39
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g14740.1 (Oryza sativa), 3'ss of exon 39
lower sequence: GLYMA07G11610.1 (Glycine max), 3'ss of exon 35
gttatttcctattttccatcaaatatccattctatt-ggattatttttttatacttgtgtaatattttatttta--tggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG
            || | |||     ||    ||| |   | | || || | | ||||||  | |||   || |   || | |||   |||||||| |   ||||||||||||| ||||| || ||| || | ||||| |||||||| || || |||||||| || ||  | ||||| |||||||| |||||||
-----------gttgctatctctcctctgcactactcaaaattttcttctgtgcttgtgctaaattcatttatgcttgttgcattaatttcagGCATCAAAATTCATTGATGAGACTGGCATAGATGCTTTGGCAGTGTGTATTGGTAACGTGCATGGAAAGTACCCTGCAAGTGGTCCAAATCTGAGATTTG

upper sequence: LOC_Os06g14740.1 (Oryza sativa), 3'ss of exon 39
lower sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 37
gttatttcctattttccatcaaat---atccattctattggattatttttttatacttgt--gtaatattttattttatggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG
|| | | |    |||| |  ||||   |  ||   || |   || | |||||| |  | |   |   ||  |  ||     |   |   || |||||  | || |||||||||||||||||||| ||| || | ||||| ||||| |||||||| ||||||||||| ||  | | ||| |||||||||||| |||
gtcactgct--ctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG
















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|29675863|gb|CB672138.1|CB672138
EST:     ATGGCTTGTCAGTCGAAGAATACGAAGCAAGATATACTGATGTTGCTCAG                         GCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
EST: gi|29676917|gb|CB673192.1|CB673192
EST:     ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAG                         GCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
EST: gi|29678971|gb|CB675246.1|CB675246
EST:     ACGAAGCAAGATTTACTGATGTTGCTCAG                         GCCTTGGAATTCATGGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: ACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
EST: gi|29672546|gb|CB668821.1|CB668821
EST:     AAGCAAGATTTNCTGATGTTGCTCAG                         GCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: AAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
EST: gi|29665309|gb|CB661584.1|CB661584
EST:     ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAG                         GCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
EST: gi|58694345|gb|CK083032.1|CK083032
EST:     ATGGCTTGACAGTCGAAGAATATGAAGCAAGATTTACTGATGTTGCTCAG                         GCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT
genomic: ATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATT

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: 40

AAAAGGCATGCTTGTAGAAGCTGAACTGGGGAGACTCTCAGGCACTGAAGATGGCTTGACAGTCGAAGAATACGAAGCAAGATTTACTGATGTTGCTCAGgttatttcct ... tatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattatttttttatacttgtgtaatattttattttatggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG
                                             tatttttc  CT-rich tract
     tatttttttatacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttcctattttccatcaaatatccattctattggattatttttttatacttgtgtaatattttattttatggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA