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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAACCAAGACCAAGAAGCAGAATGCCCCAGCGAAGCTCTACCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcacgtgaaactacttctttgcatagcttcttgtccttgttatgccttgcgatgctagaagctttaaatgcactgctatgaacataaagcatcc...

Basic information

species Oryza sativa
transcript LOC_Os05g46430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G088060_T04 (Zea mays), 5'ss of exon 3
CACAACCAAGACCAAGAAGCAGAATGCCCCAGCGAAGCTCTACCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcacgtgaaactacttctttgcatagcttcttgtc---cttgttatgccttgcgatgctagaagctttaaatgcactgctatgaacataaagcatcc
 || ||||||||||||||||||||  | || |||||||||  |||||||||||| |||||||||||||||||||| ||||| |||||||| || ||||||||| | |||| || || | | |  | |  |  ||   ||       ||| |   ||||  |||||| |  ||  ||   ||  ||| |   | | | |     
TACTACCAAGACCAAGAAGCAGAACACACCCGCGAAGCTCAGCCACAAGTCTGTAATGCGCAAGGAGTTCCGCAAGATGGCCAAGGCTGTGAAAAACCAGgtagtggcacatggaaatgcataat-gtttgtctctatgggggatatgtgagtgcttgttatgctacatactgcaag-acatagctcttg-ctttatgtgctg

upper sequence: LOC_Os05g46430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G394827_T02 (Zea mays), 5'ss of exon 3
CACAACCAAGACCAAGAAGCAGAATGCCCCAGCGAAGCTCTACCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcacgtgaaactacttctttgcatagcttcttgtccttgttatgcc--ttgcgatgctagaagctttaaatgcactgctatgaacataaagcatcc-
 || |||||||||||||||||||| || || |||||||||  ||||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||||| |||||| || ||  || | | ||| |   |    |    | |        |||   |||||   ||  |   ||  ||  | |    ||     ||   
TACTACCAAGACCAAGAAGCAGAACGCACCTGCGAAGCTCAGCCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAGATGGCCAAGGCTGTGAAAAACCAGgtactagcacatggaatcacat-tatgcttgattgtacggtaatatggcagtgtttgttttgctact-gcaatgcgtg-gcttttttatgtattggatattgt
















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|4716506|gb|AU057622.1|AU057622
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|55434653|gb|CV730451.1|CV730451
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86901942|gb|CI298589.1|CI298589
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTG
EST: gi|33672454|gb|CF300693.1|CF300693
EST:     CTGTGATGCGCAAGGAGTTCCGCANAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|58599291|gb|CK009819.1|CK009819
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|33677297|gb|CF305536.1|CF305536
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|38474214|gb|CF958346.1|CF958346
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|88975661|gb|CI021743.1|CI021743
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86592782|gb|CI268447.1|CI268447
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|55432164|gb|CV729101.1|CV729101
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|33685743|gb|CF313982.1|CF313982
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86595615|gb|CI266512.1|CI266512
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|55437121|gb|CV731758.1|CV731758
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86511813|gb|CI154446.1|CI154446
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|88329547|gb|CI648610.1|CI648610
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTA
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTA
EST: gi|55439318|gb|CV732963.1|CV732963
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86901100|gb|CI306289.1|CI306289
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTAC
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTAC
EST: gi|88238562|gb|CI238411.1|CI238411
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|8528354|gb|AU093169.1|AU093169
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|86257170|gb|CI061933.1|CI061933
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|88335297|gb|CI650262.1|CI650262
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGANAACTACTACAGGCCTGACC
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACC
EST: gi|88569753|gb|CI660928.1|CI660928
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTAC
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTAC
EST: gi|88211306|gb|CI210946.1|CI210946
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|88345220|gb|CI628474.1|CI628474
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTG
EST: gi|88210653|gb|CI210502.1|CI210502
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
EST: gi|87017330|gb|CI301366.1|CI301366
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACA
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACA
EST: gi|66912719|gb|CX099567.1|CX099567
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGGCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGG
EST: gi|396941404|gb|HO188613.1|HO188613
EST:     CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAG                         GTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG
genomic: CTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGG

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: 74 (upstream exon), 64 (downstream exon)
Score: 103

CACAACCAAGACCAAGAAGCAGAATGCCCCAGCGAAGCTCTACCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcac ... tgcccttcagGTGAGTGACAACTACTACAGGCCTGACCTGACCAAGCCGGCTCTTGCGAGGCTTAGCTCAGTGTACCGCAGCCTCCAGGTTTCCAAGTCTGGTGCCAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAACCAAGACCAAGAAGCAGAATGCCCCAGCGAAGCTCTACCACAAGTCTGTGATGCGCAAGGAGTTCCGCAAAATGGCTAAGGCTGTCAAGAACCAGgtattagcacgtgaaactacttctttgcatagcttcttgtccttgttatgccttgcgatgctagaagctttaaatgcactgctatgaacataaagcatcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC