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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTACTACCGACGTGGAGCGGCATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtttgttttcctagttttgtggtctcttcccagattgagtgattgagaatgactatttctagtcacttttcttgcttttcttggtgctgctttatattaatgttggtgaccatctagggatagcaggaaccacattattttgtttcatgtggtacattaataagtctacttttctttctag

Basic information

species Oryza sativa
transcript LOC_Os05g11550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11550.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G126435_T02 (Zea mays), 5'ss of exon 3
GGTTACTACCGACGTGGAGCGGCATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtttgttttcctagttttgtggtctcttcccagattga-gtgattgagaatgactatttctagtcacttttcttgcttttcttggtgctgctttatattaatgttggtgaccatctagggatagcaggaaccacattattttgtttcatgtggtacattaataagtctacttttctttctag
||||| ||  |||| || || || |||||||||||||| |||||||||||||| |||||||||||||| |||||  |||   || |   |||  | |||   || | |  |  |    ||||   ||| |   |||| | | |             | | |||  |||  |  ||  || |  |  ||   |||||   | |  || || ||    || || |  ||                                  
GGTTATTATAGACGAGGCGCAGCTTATCTTGCCATGGGAAAGTTCAAGGAAGCCCTGAAGGATTTTCAGCAGgttagcaaactgct---ctacctgtgtacactgtacatatctccttgtgacctagactacttattaccaata------------tatattg--gctagtcaattctattacttttggatatctattaa-attagaaaaca----atcttttcccag---------------------------------
















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|33794510|gb|CF323142.1|CF323142
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
EST: gi|58687860|gb|CK076547.1|CK076547
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
EST: gi|29630243|gb|CB635252.1|CB635252
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
EST: gi|58671706|gb|CK060392.1|CK060392
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGGCCTAATGATCCAGATGC
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGC
EST: gi|29676952|gb|CB673227.1|CB673227
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
EST: gi|29681334|gb|CB677609.1|CB677609
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
EST: gi|66920389|gb|CX107237.1|CX107237
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCA
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCA
EST: gi|33793725|gb|CF322745.1|CF322745
EST:     CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAG                         GTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG
genomic: CATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAG

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: 72 (upstream exon), 71 (downstream exon)
Score: 34

GGTTACTACCGACGTGGAGCGGCATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtt ... ttctttctagGTGAAAAGAATCAGCCCTAATGATCCAGATGCTACTAGGAAATTGAAAGAGTGTGAGAAAGCTGTCCAGAAAATCCGTTTTGAAGAGGCAATTTCTGTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTACTACCGACGTGGAGCGGCATATCTTGCCATGGGTAAGTTCAAGGAAGCTCTGAAGGATTTTCAACAGgtgcgcagtttgttttcctagttttgtggtctcttcccagattgagtgattgagaatgactatttctagtcacttttcttgcttttcttggtgctgctttatattaatgttggtgaccatctagggatagcaggaaccacattattttgtttcatgtggtacattaataagtctacttttctttctag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG