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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcatatagctatctaaatcattttaaacttcatcaac...

Basic information

species Oryza sativa
transcript LOC_Os03g13970.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147671_T02 (Zea mays), 5'ss of exon 6
TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTG---ATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcatatagctatctaaatcattttaa--acttcatcaac
 |||||||    | |||||||||||||||||   |||||||||||||| ||||| |||| |||||||||||||||||    ||| ||  |||| ||||| |||||||| ||  | |   || ||  ||||          |||| | |    |   |  |   |||    |    |   | | |  || ||   |||      | 
CGAAAATAT---CAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcagtttatcactgtccatcagt-tgaaactaaaaatgccctgacctgcctcaaatgcttcaagttttgatgactggttgtatgtactctcctga-

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G165926_T02 (Zea mays), 5'ss of exon 6
TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcata-tagctatctaaatcattttaaacttcatcaac
|  | |  |  || ||| | |||||||||||  ||||||||||||||| ||||  |||||||||||||||||||||| || | | ||||| || || |||||||| ||  | |||   |||||   |  | |   ||       ||            | | ||  ||  || |   |  |    |  |  ||||      
TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcactgtccataagttacaaacta-aaaatgccctaacctgtctccaatacttgaagttttagcagttgcatgtactcatgaactcttctctgtg
















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|218485696|gb|FG969920.1|FG969920
EST:     AAGCGGAACTTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|5055982|gb|AU075361.1|AU075361
EST:     AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|218483651|gb|FG955547.1|FG955547
EST:     AAGCGGAACTTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|33657882|gb|CF280496.1|CF280496
EST:     AAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|33801681|gb|CF326712.1|CF326712
EST:     AAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|88247152|gb|CI247001.1|CI247001
EST:     CTGATGATAAAAAAGATCACCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: CTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|44670518|gb|CR283952.1|CR283952
EST:     GAACTTGCCTCAAATGCTGCTGATGATAAAAAGGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: GAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|58675750|gb|CK064437.1|CK064437
EST:     AAGCGGAACTTGCCTCATATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|29678148|gb|CB674423.1|CB674423
EST:     AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|88840095|gb|CI079549.1|CI079549
EST:     TGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: TGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|58607467|gb|CK035500.1|CK035500
EST:     GCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         T
genomic: GCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacag-
EST: gi|58607467|gb|CK035500.1|CK035500
EST:     GCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         T
genomic: GCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacag-
EST: gi|88245959|gb|CI245808.1|CI245808
EST:     GCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: GCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
EST: gi|6449564|gb|AU081506.1|AU081506
EST:     AAGCGNAACCTGCCTNAAATGCTGCTGATGATAAAAAAGATCAGCCGAAG                         GAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG
genomic: AAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAG

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), 59 (downstream exon)
Score: 31

TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgt ... gtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGCGGCTGATGCTGCTATGGCAGAGGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcatatagctatctaaatcattttaaacttcatcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA