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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactatgtcatatatttgtggactgactagtagtttttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 19
aactatgtcatatatttgtggactgactagtagttt----ttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG
   | | |  | || | | |     || |||   |     |    |  |  |  |||  ||  | ||  | |   ||||||  ||| |  |   ||||||||||||||||||||||||| |||||||||| |||||||| |||   |||||||||||||| ||||||||||||||||   ||||| ||||   || ||||||||
---ttttttttttactcgagagagtacgagtgcctgaaaatagggagaaccgatgagtgatattttgcgtatttaatttattagttattgt-tgtgtcctgcagGGGAAAGGTGAATTTTCGATGGAGTATCTGGAGCACAATACCGTATCGCAGGATGTACAGATGCAACTAGTGAATACGTACAAGGCCAGCAGGGGCACAG
















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|32933717|gb|CF038529.1|CF038529
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTGCGATGGAGTA
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTA
EST: gi|84980317|gb|DW530666.1|DW530666
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
EST: gi|32932818|gb|CF037630.1|CF037630
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTACGATGGAGT
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGT
EST: gi|211492457|gb|FL459662.1|FL459662
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
EST: gi|33093919|gb|CF053913.1|CF053913
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGTGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCT
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCT
EST: gi|61119855|gb|DN560816.1|DN560816
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
EST: gi|69351603|gb|DR452190.1|DR452190
EST:     CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAG                         GGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG
genomic: CGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 148

GTTCCGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 76

GTTCCGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GTTCCGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

GTTCCGCTAAACAATATGTTTGGATATGCAACAGCTATTCGATCAGCGACTCAGgtaaatatac ... tgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG
                         tatttatctgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactatgtcatatatttgtggactgactagtagtttttataaatattggagagaaattgtgtggttttcctatttatctgttttcttgcatgtcctgcagGGGAAAGGTGAATTTACGATGGAGTACCTGGAGCATAATGTTGTATCGCAGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG