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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACCAGTGAAGAACTCATCAAAGTAACTGAAGAACAACTAGCTGCGTCTGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacattttctttgtgccatttcttcaattaggtacacatgttcagtattcataagataaattgtgcagattgtcttatgttgcatgacattttcc...

Basic information

species Oryza sativa
transcript LOC_Os11g37130.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g37130.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G898735_T02 (Zea mays), 5'ss of exon 5
TACACCAGTGAAGAACTCATCAAAGTAACTGAAGAACAACTAGCTGCGTCTGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacattttctttgtgccatttcttcaattaggtacacatgttcagtattcataaga--taaattgtgcagattgtcttatgttgcatgacattttcc-
|| || || || ||||| || |||||||||||||||||| | ||||| || || ||||||||||||||| | ||| | ||| |  | || || ||  |||||   | |||||      | | | |  | || ||   |  || | || |||||| | |  |  | |||| || | |   || ||  |||  |  |        
TATACTAGCGAGGAACTAATGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCTGCTTGGAATCCACAACAGCCTGCCACGTCGCAACAGCAAGgtca-ggcatttctagacttctagtcttgcagtttcttgaac-tatttagtatttacagtacctgaatt-tgtaaaggctcctagtttgtgtttccccgcgtt
















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|86532923|gb|CI173129.1|CI173129
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCATAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88995472|gb|CI022795.1|CI022795
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTGCTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|313080741|gb|HO213538.1|HO213538
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|94363039|gb|CI053200.1|CI053200
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88564669|gb|CI495386.1|CI495386
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88508300|gb|CI435806.1|CI435806
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88563245|gb|CI493962.1|CI493962
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCACCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|29663432|gb|CB659707.1|CB659707
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88901813|gb|CI374421.1|CI374421
EST:     CTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: CTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88691337|gb|CI733921.1|CI733921
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAG
EST: gi|88515985|gb|CI443639.1|CI443639
EST:     TGCAGCTGCTGCTTGGAATACTCAAGGACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|29656570|gb|CB652845.1|CB652845
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCCCAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88564530|gb|CI495247.1|CI495247
EST:     TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
EST: gi|88689432|gb|CI733008.1|CI733008
EST:     TGCAGCTGCTGGTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAG                         AAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG
genomic: TGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTG

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: 31 (upstream exon), 69 (downstream exon)
Score: 3

TACACCAGTGAAGAACTCATCAAAGTAACTGAAGAACAACTAGCTGCGTCTGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacat ... catatttcagAAGCAGCAGCTACTTCTGAAAGTAATGACGGTGCTATATCAAGAGGGAGTGATGGTGCTGGTGCTGCAATGAGTGAGCCCAATCGGAACATTTCTGAGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACACCAGTGAAGAACTCATCAAAGTAACTGAAGAACAACTAGCTGCGTCTGCAGCTGCTGCTTGGAATACTCAAGAACCTCCTCCATCACAGCAAAAAGgttttgacattttctttgtgccatttcttcaattaggtacacatgttcagtattcataagataaattgtgcagattgtcttatgttgcatgacattttcc

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC