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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcatcatgctatttttttttagctttttgtgcatctgcttggagatattgttgtc...

Basic information

species Zea mays
transcript GRMZM2G085670_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatat--tgttgtc
||||||||||||||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
AATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G085670_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatatt--gttgtc
        ||||||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
--------CAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G085670_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatatt--gttgtc
           |||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
-----------GCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

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|32927438|gb|CF032250.1|CF032250
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211111835|gb|FL481580.1|FL481580
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927397|gb|CF032209.1|CF032209
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32934734|gb|CF039546.1|CF039546
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|71764777|gb|DR962714.1|DR962714
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCTGACCAAAGAG                         GAGGCGACTACCACTGGCGT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGT
EST: gi|16925930|gb|BM078998.1|BM078998
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211195517|gb|FL100641.1|FL100641
EST:     GGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927878|gb|CF032690.1|CF032690
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|50325880|gb|CO521006.1|CO521006
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32933246|gb|CF038058.1|CF038058
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927819|gb|CF032631.1|CF032631
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927866|gb|CF032678.1|CF032678
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927641|gb|CF032453.1|CF032453
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|32927565|gb|CF032377.1|CF032377
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCATTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|78090434|gb|DV518808.1|DV518808
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211226565|gb|FL435978.1|FL435978
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|78090435|gb|DV518809.1|DV518809
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCTACAATGGGAACTGCTGATACCTTGATTGAGACATTTTGACGCCAGAGCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98

AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCTACAATGGGAACTGCTGATACCTTGATTGAGACATTTTGACGCCAGAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCTACAATGGGAACTGCTGATACCTTGATTGAGACATTTTGACGCCAGAGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCTACAATGGGAACTGCTGATACCTTGATTGAGACATTTTGACGCCAGAGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcatcatgctatttttttttagctttttgtgcatctgcttggagatattgttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA