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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctcttctgcttctgctcgaggctcctcctcctgctgctgttcccagttcaccacgagcgtaacgtggatggtttgtccttttgttctggtaccag

Basic information

species Zea mays
transcript GRMZM2G118586_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112015_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 2
GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgt-----att----ctcttctgc-ttctgctcg--aggctcctcctcctg---------------------ctgctgttcccagttcaccacgagcgtaacgtggatggtttgtccttttgttctggtaccag
|| ||||||||||| ||||| ||||| |||||  |||||||||||||||| || |||||||| |||||     ||      || | ||| ||||| ||   | | ||  | | |||                      | ||||   | || | ||| ||| ||||  |   | |  |||   |||| | |    ||||
GCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAGgtcaaggatcaccattcctttgcattctgatcaccatgttctccatgctgaaatttgccttcatagatcattttctgtcttctgtcctccatgagtgtaatttaatttgcgtgtgtgtttgctttacctccag

upper sequence: GRMZM2G112015_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G11740.1 (Glycine max), 5'ss of exon 2
GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctcttctgcttctgctcgaggctcctcctcctgctgctgttcccagttcaccacgagcgtaacgtggatggtttgtccttttgttctggtaccag
|| |||||| ||||||| ||| | |||||||| |||||||| || ||||| || |||||||||||||||| | ||||| | |   | | |  |||    |  || |  | ||| ||       |  | |      ||  | |||  ||  || | | |||| ||||
GCAAATACGTTGCGGTTATACTTGACCTGCATTCGGAACACGCTCGAGGCCGCAATGTGCCTCCAGgtat-cacttcttcgttaacgccactctcaatatt-tgtttattttcgcatcgataaataatcacgtgttgtgttgttcttc--ttcgctatggttccag

upper sequence: GRMZM2G112015_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G28650.1 (Glycine max), 5'ss of exon 2
GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtatt--ctcttctgcttctgctcgaggctcctcctcctgctgctgttcccagttcaccacgagcgtaacgtggatggtttgtccttttgttctggtaccag
|| |  ||| ||||||| ||| | |||||||| |||||||| || ||||| || ||||||||||||||||     ||||| | | |  |   |  ||  |    |  |    |   | ||||    |    ||   || | |  ||| | |||  | | || | ||||
GCAAGCACGTTGCGGTTATACTTGACCTGCATTCGGAACACGCTCGAGGCCGCAATGTGCCTCCAGgtatcactccttcttcgtttcttttggcatcaacaaaataatcacctcttctgttctgttc---tgttctgttgtttttttcttcttc-gctatgcttccag

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|85152679|gb|DW587816.1|DW587816
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|28188265|gb|CB179875.1|CB179875
EST:     GTACCATCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: GTACC-TCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|32925177|gb|CF029989.1|CF029989
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|21432169|gb|BQ547659.1|BQ547659
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|60346160|gb|DN213133.1|DN213133
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|211438327|gb|FL007592.1|FL007592
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|32925995|gb|CF030807.1|CF030807
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|211435743|gb|FL007591.1|FL007591
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
EST: gi|37376615|gb|CF624854.1|CF624854
EST:     TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG                         AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC
genomic: TGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 98

GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 126

GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctctt ... ctggtaccagAATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAGgtattctcttctgcttctgctcgaggctcctcctcctgctgctgttcccagttcaccacgagcgtaacgtggatggtttgtccttttgttctggtaccag

- - - - - - - - - - - - - - - - - - - - -  TGGAGG