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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtcttcacgtttagtttaggtttagttatcatttgtgaaaagatcgctatatctgcaatattcactcatctgttaatgaaaccttttattaaccc...

Basic information

species Zea mays
transcript GRMZM2G044457_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044457_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g41120.2 (Oryza sativa), 5'ss of exon 10
---------------------------------GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtcttcacgtttagtttaggtttag-----ttatcatttgtgaaaagatcgc--tatatctgcaatattcactcatctgttaatgaaaccttttattaaccc
                                 || ||||| |||||||||| ||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||   | | || | || ||||   | |      |||   ||| | |    || |   |  ||  |   |||    |||    | | | | |  || |        
AAAATCTTAGTTCTCCACCTTATGTTTTTGCAGGTAATATTTACAGAAGAAAATAGTTCCCTGCTCCACTATCTGACGAACCTATGTGCTATAGTGGGAGgtattagcattacctctattttattctcaaactgattaatcttttttattctattgtagtgaatgagtgttatctcttcagtcttcactaacaaattctt-------

upper sequence: GRMZM2G044457_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 5'ss of exon 12
GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtcttcacgtttagtttaggtttag-----ttatcatttgtgaaaagatcgctat--atctgcaatattcactcatctgttaatgaaaccttttattaaccc
|| ||||| |||||||||| ||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||   | | || | || ||||   | |      |||   ||| | |    || |   |  ||  |   |||    |||    | | | | |  || |        
GTAATATTTACAGAAGAAAATAGTTCCCTGCTCCACTATCTGACGAACCTATGTGCTATAGTGGGAGgtattagcattacctctattttattctcaaactgattaatcttttttattctattgtagtgaatgagtgttatctcttcagtcttcactaacaaattctt-------
















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|148944283|gb|EC889379.2|EC889379
EST:     AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|149111501|gb|EE295004.2|EE295004
EST:     AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|60346135|gb|DN213108.1|DN213108
EST:     AAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|50334990|gb|CO530116.1|CO530116
EST:     AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|211172233|gb|FL456933.1|FL456933
EST:     AAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|91873242|gb|EB403199.1|EB403199
EST:     AAGTAGATCCCTACTCCACTCCCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|149027083|gb|EE046394.2|EE046394
EST:     AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|211541072|gb|FL347103.1|FL347103
EST:     AAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
EST: gi|4572792|gb|AI586441.1|AI586441
EST:     AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA
genomic: AAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGA

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: 79

GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGAAGGCACTCAAGAAGAAAATGGAGCTAGGTAAATACAGATGATCAACATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGAAGGCACTCAAGAAGAAAATGGAGCTAGGTAAATACAGATGATCAACATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 187

GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGAAGGCACTCAAGAAGAAAATGGAGCTAGGTAAATACAGATGATCAACATC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 113

GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtctt ... tgattttcagGTGTGTTCACTGTCTCGGGTATCATCGACTCGTTTATATACCACGGACAGAAGGCACTCAAGAAGAAAATGGAGCTAGGTAAATACAGATGATCAACATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATATTCACAGAAGAAAGTAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatggtcttcacgtttagtttaggtttagttatcatttgtgaaaagatcgctatatctgcaatattcactcatctgttaatgaaaccttttattaaccc

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