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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgccgctgacccacaacccattatgccattcggtcctcccccaccttttttggttgcacggttgcctgacagcgggcacaaataaactagcaaccaaagcggccctttattttattctgggtgtgctcctaccggccgcacatgttaagctcacaagcacatcgctgctgttgacgttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC

Basic information

species Zea mays
transcript GRMZM2G421791_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 8
gtattgccgctgacccacaacccattatgccattcggtcctcccccaccttttttggttgcacggttgcctgac--agcgggcacaaataaactagcaaccaaagcggccctttattttat-tctgggtgtgctcctaccggccgcacatgttaagctcacaagcacatc----gctgctgtt-gacgttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC--
           |   | || || | ||    |||      | | |   |||  | ||   || |    |   ||  | |  ||| || ||||||| ||         ||||| |||||  | | |     ||     ||  |  | || |  |||||| || ||   |||      ||||||| ||| |  |||||||  |||||||| |||||||| ||||| ||||||||||| ||| ||| ||||||| |   |||    |      |   || |    ||  |  |  ||     
-----------gtttctcatcctactacataatttttgttttcacatacttcctaggacacaagcacacactacctaacctgcagaactaaactaccagt-------gccctgtatttcctgtgtcctattggcagcacatgttgaacctcataagcttactagtgtatctgtttttgctgtttgacatcacaccagGGATACCACAGGGAGCTACTAGAGCAAATGATTGCATCCGGTTGGAAGCCCCCTCCAACGGCCAGTGAACCATCT--CGAAAACTCAGATTAGGTAGCAGGA
















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|33096912|gb|CF056872.1|CF056872
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGA
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGA
EST: gi|13149974|gb|BG320296.1|BG320296
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTASNGNATYC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAG-G-ATGC
EST: gi|149096257|gb|EE181965.2|EE181965
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|31357415|gb|CD441772.1|CD441772
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|21759893|gb|BQ635434.1|BQ635434
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|45568659|gb|CK986172.1|CK986172
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|16921217|gb|BM075042.1|BM075042
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|149087532|gb|EE176930.2|EE176930
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|149097874|gb|EE183808.2|EE183808
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|211343960|gb|FL066590.1|FL066590
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCC
EST: gi|111991041|gb|EE331929.1|EE331929
EST:     GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAG                         GCGTACCACTTTATAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCC
genomic: GGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAG-AGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCC

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: 45 (upstream exon), 45 (downstream exon)
Score: 12

CCAAATAAGTTTCAGCACCGTCCGGGACAAAATCAGGGCTAGAGTTGGCTGGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 32

CCAAATAAGTTTCAGCACCGTCCGGGACAAAATCAGGGCTAGAGTTGGCTGGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

CCAAATAAGTTTCAGCACCGTCCGGGACAAAATCAGGGCTAGAGTTGGCTGGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

CCAAATAAGTTTCAGCACCGTCCGGGACAAAATCAGGGCTAGAGTTGGCTGGATGCCCGAGATGTTCATGGACTGCGAGAGGCGCAACTTTGTCGTTCAGgtattgccgc ... gttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accggccgcacatgttaagctcacaagcacatcgctgctgttgacgttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC
                                      tgttgac  putative branch site (score: 70)
           atgttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgccgctgacccacaacccattatgccattcggtcctcccccaccttttttggttgcacggttgcctgacagcgggcacaaataaactagcaaccaaagcggccctttattttattctgggtgtgctcctaccggccgcacatgttaagctcacaagcacatcgctgctgttgacgttgcaccagGCGTACCACAGAGAGCTACTGGAGCAGATGATTGCATCAGGTAGGATGCCCCCTTCGGGGGCTGTGGTGGTGACCGACGCAGCACCATCTCGGAAAGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG