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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatttgcttcgctgtcaactgcatgaggttttgaaattttgagtagcagtagctgcattacttaatctgtgaatcggtaccatgctttagttca...

Basic information

species Zea mays
transcript GRMZM2G125556_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 5'ss of exon 2
ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaact--catttgcttcgctgtcaactgcatgaggttttgaaattttgagtagcagtagctgcattacttaatctgtgaatcggtaccatgctttagttca
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ACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGTCTGCAAGCAAATCTTGCCTGTTTTGGgtaactgtctttgatttccatattcagatca-gtagcttggttccttttttaatttgtatttactatgtttagttca-gtactgcggtggagcagtaaatgg
















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|211475755|gb|FL124812.1|FL124812
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|76285485|gb|DV025053.1|DV025053
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|93282355|gb|EB674619.1|EB674619
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041272|gb|FL124819.1|FL124819
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211464236|gb|FL298400.1|FL298400
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041278|gb|FL124825.1|FL124825
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211464240|gb|FL298404.1|FL298404
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041276|gb|FL124823.1|FL124823
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|60400894|gb|DN233701.1|DN233701
EST:     TCTCACCAAGCCTTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211464238|gb|FL298402.1|FL298402
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211466770|gb|FL298415.1|FL298415
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041277|gb|FL124824.1|FL124824
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041274|gb|FL124821.1|FL124821
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211475759|gb|FL124816.1|FL124816
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211475756|gb|FL124813.1|FL124813
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041273|gb|FL124820.1|FL124820
EST:     TCTCACCAAGCCCTTCCTTGAT-TCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211041271|gb|FL124818.1|FL124818
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211466771|gb|FL298416.1|FL298416
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
EST: gi|211464237|gb|FL298401.1|FL298401
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCG                         ATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATA

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), 48 (downstream exon)
Score: 140

ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATATCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATATCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATATCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatt ... tatggaccagATAAATTTGGAGGTGCTATGGCAATTGTAAAGAGTGATATCGGCGGCAATATCACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATATTGCCTGTCCTCGgtaactcatttgcttcgctgtcaactgcatgaggttttgaaattttgagtagcagtagctgcattacttaatctgtgaatcggtaccatgctttagttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA