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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagttggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattcttggtagaaaaaagatttgagttcctccacattgtttcattttcag

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 9
TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagttggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattcttggtagaaaaaagatttgagttcctccacattgtttcattttcag
||| || |||||  |||||||  |||||| ||||| |||||||||  |||||||||||||||| ||||| ||||||||||  |||||||||||||||||||||||||  | ||  ||| || | ||   | ||||||       ||| | ||   ||||   ||| |  |||      |||| ||  ||  | |  |   |||| |||
TAGAGCTCCTAAAATGGGCAACCCTCGTAGAGATGAGAAGCCTGATAATTTTGCTCGTGAAGCCAAGGAATTCTTGCGCACAAGGTTGATTGGCAAGCAAgtatgtacataggttttgagatattccatcagaagttc------cataacaagttgttacctttgttgaaaattta--ttgattttttctccttcct---atttccag
















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|18384788|gb|BM417987.1|BM417987
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATTGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|9566452|gb|BE475961.1|BE475961
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAAATACTCTCGAAGGATCAGCACCGTGGATGGACA
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGG-AATATTCTCGAAGGATCAGCACCGTGGATGGACA
EST: gi|16746003|gb|BM032433.1|BM032433
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|21390058|gb|BQ528107.1|BQ528107
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|18385299|gb|BM418498.1|BM418498
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|13150309|gb|BG320631.1|BG320631
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTDGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|22489141|gb|BU049064.1|BU049064
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|18384789|gb|BM417988.1|BM417988
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|18384787|gb|BM417986.1|BM417986
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|211479964|gb|FL426378.1|FL426378
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCCCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|88758397|gb|DY542766.1|DY542766
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|211277470|gb|FL423592.1|FL423592
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|211005422|gb|FL371735.1|FL371735
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCCCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|211311595|gb|FL416730.1|FL416730
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATACTCCCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
EST: gi|60394760|gb|DN227630.1|DN227630
EST:     TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAA                         GTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG
genomic: TTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAG

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: 43 (upstream exon), 48 (downstream exon)
Score: 152

TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAGAGTGTTGCTCCAACAGCAAACATTGCTGATACAAGAGTATTAGATTATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 161

TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAGAGTGTTGCTCCAACAGCAAACATTGCTGATACAAGAGTATTAGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAGAGTGTTGCTCCAACAGCAAACATTGCTGATACAAGAGTATTAGATTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagtt ... tcattttcagGTGGCTGTTGAAATGGAATATTCTCGAAGGATCAGCACCGTGGATGGACAGAGTGTTGCTCCAACAGCAAACATTGCTGATACAAGAGTATTAGATTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGGCCCCTAAGTTGGGCAATGCTCGTACAGATGTGAAGCCTGACCATTTTGCTCGTGAAGCTAAGGAGTTCTTGCGCATGAGGTTGATTGGCAAGCAAgtatgtagttggggcttgtgacaatctggctgaagtttttaattcatcataaacagttattcttggtagaaaaaagatttgagttcctccacattgtttcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA