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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccctctcgccccgcgggagctcccctgtcccgggctggagagtttagtgaccgggatctgattagttcctgtcgcgccttgcttagcatttcga...

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 1
CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgc---ccctctcgc-cccgcgggagctcccctgtcccgggctggagagtttagtgaccgggatctgattagttc--ctgtcgcgccttgcttagcatttcga-
 |||||||||||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||| || |||||||||||| ||||||||||||| |||    |||||| | ||||  | || |||||||  ||||| ||  |        | | |||||||||   |||   ||| |   | | |||| | |||||   
TTACCTCAAGCGGCCGAAGCGCCTCGCCCTCCTCTTCTTCGTCTTCGTCGCCGCCACCTTCGCCTTCTGGGATCGACAGTCGCTCGTCCGCGAGTACGAGgttcgcgcctcctctcccacccgttgaagttcccctgatccgggttgagg-------cggcggggatctgaccggttttgctgcccgccttagcttcggatttcctt
















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|148937008|gb|EC881178.2|EC881178
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|148934064|gb|EC878076.2|EC878076
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|149108157|gb|EE292504.2|EE292504
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|211506494|gb|FL158303.1|FL158303
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCGCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTC-CCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|211508842|gb|FL158306.1|FL158306
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|148930753|gb|EC873061.2|EC873061
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|19058210|gb|BM736877.1|BM736877
EST:     CAGCCACCTTCGCCTTCTGGGNCCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|18964229|gb|BM660885.1|BM660885
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|20300875|gb|BQ163818.1|BQ163818
EST:     CAGCCACCTTCGCCTTCTGGGNCCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|20301029|gb|BQ163972.1|BQ163972
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|149073799|gb|EE162117.2|EE162117
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|87151942|gb|DY396731.1|DY396731
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|78112348|gb|DV530742.1|DV530742
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|20300848|gb|BQ163791.1|BQ163791
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|87153018|gb|DY397807.1|DY397807
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|19057740|gb|BM736407.1|BM736407
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|22490422|gb|BU050345.1|BU050345
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|18964227|gb|BM660884.1|BM660884
EST:     CAGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
EST: gi|211506492|gb|FL158301.1|FL158301
EST:     CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAG                         TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG
genomic: CGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG

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), 47 (downstream exon)
Score: 112

CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 141

CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 158

CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccct ... ctattttcagTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACCTCAAGCGGCCCAAGCGCCTGGCGCTCCTCTTCTTCGTCTTCGTCGCGGCCACCTTCGCCTTCTGGGACCGCCAGTCGCTCGTCAGCGAGTACGAGgtgcgcccctctcgccccgcgggagctcccctgtcccgggctggagagtttagtgaccgggatctgattagttcctgtcgcgccttgcttagcatttcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgtcc