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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctacacttgaactgtcaaatatgtttatttattcacatttgagcttgtctttatctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC

Basic information

species Oryza sativa
transcript LOC_Os07g36470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019999_T01 (Zea mays), 3'ss of exon 7
atctacacttga-actgtcaaatatgtttatttattcacatttgagcttgtctttat-ctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC
|| |  |  |    | ||  | |||||       || |   |||    ||| |||   |  |||||  || ||  |  | ||  ||  |  |||||||||||||| | |||||||| |||||||| |||||  | ||||||||||| ||||| |||||||||||||| ||||| |||||||| || |||||||||||||| |
atgtgaatgtatcgccgtttagtatgtgctcaggttga-gcttgtatgtgtttttgcacctttttgtgctaactgcaat-ttgctattatttatgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC

upper sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G163233_T04 (Zea mays), 3'ss of exon 10
atctacacttgaac-tgtcaaatatgtttatttattcacatttgagct---tgtctttat-ctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC
    | || ||||  | || | | | || ||||  |||  ||     |   ||| |||   |  |||||  || ||| |  | ||  ||  |  ||| || ||||||| | ||||||||  ||||||| |||||  | ||||||||||| ||||| |||||||||||||| ||||| |||||||| || |||||||||||||| |
---aaaacgtgaatgtatctagtctatt-atttgctcaggttgagattgtatgtttttgcacctttttgtgctaacagcaat-ttgctattatttatacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC
















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|218491215|gb|FG953120.1|FG953120
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|38479045|gb|CF963178.1|CF963178
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|38483054|gb|CF966856.1|CF966856
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|29688877|gb|CB685152.1|CB685152
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|58684033|gb|CK072720.1|CK072720
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|11442551|gb|BF430454.1|BF430454
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|58682821|gb|CK071508.1|CK071508
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAG
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAG
EST: gi|218495142|gb|FG957786.1|FG957786
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAACTAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
EST: gi|58687201|gb|CK075888.1|CK075888
EST:     GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT
genomic: GACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTT

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), 74 (downstream exon)
Score: 71

CCGTAACTTGCTTGCAAAGGGTGCGTTTGCTGCCCAAATGATTGATCTTGGACTGCCACACATAGTACAGAATTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtctttatctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC
                   aactgac  putative branch site (score: 71)
                              ttcttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctacacttgaactgtcaaatatgtttatttattcacatttgagcttgtctttatctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - -tgaactg
- - - - - - - - - - - - - - - - - - acatttg