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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcctatggttcatttgtactgggaagatattttattatctcatggcctagaacagttaaatatgacacttatttctggtacag

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 14
GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcctatggttcatttgtactgggaagatattttattatctcatggcctagaacagttaaatatgacacttatttctggtacag
||||||||| |||| ||||||||||||||||||||||| ||||| ||||||||||||||||| || ||||||||||  |     ||| | |  |||||  | | |||         ||||    ||      |||   |   | |||||   | |||
GCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCCTGGATGAATGATTTTATCCGCCAgtaagttctgaccaggcatatct--tgggactaaagttt---------tggcaagaaaggagataatgaaaatttcatttcgcatgcag

upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 14
GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcctatggttcatttgtactgggaagatattttattatctcatggcctagaacagttaaatatgacacttatttctggtacag
||||||||| |||| ||||||||||||||||||||||| ||||| ||||||| ||||||||| || |||||||||   ||||  ||| | | ||||||       |||  ||    | | | ||||       ||   | | |||||||| || |||
GCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCGTGGATGAGTGATTTTATCCGCCAgtaagttgtcatggagcatgtatcctggga-------ttagaattatgttgacaagaaggtgattatggtaaatttatttctcgtgcag
















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|74235054|gb|DT642968.1|DT642968
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAAACATCA-CGTGGCTGTACAGACTGAACATGGATTGT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAA-CATCAACGTGGCTGTACAGACTGAACATGGATTGT
EST: gi|71761137|gb|DR959074.1|DR959074
EST:     CAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
genomic: CAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
EST: gi|76932163|gb|DV172956.1|DV172956
EST:     AAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
genomic: AAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
EST: gi|71333154|gb|DR803611.1|DR803611
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
EST: gi|32840355|gb|CD980036.1|CD980036
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACGTCAACGTGGCTGT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGT
EST: gi|32938642|gb|CF043461.1|CF043461
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGT
EST: gi|32932311|gb|CF037123.1|CF037123
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTAC
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTAC
EST: gi|211011840|gb|FL066266.1|FL066266
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
EST: gi|78091151|gb|DV519525.1|DV519525
EST:     CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA                         ATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT
genomic: CGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTT

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: 89

GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcct ... tctggtacagATACCACAATGTGAACATCAACGTGGCTGTACAGACTGAACATGGATTGTTTGTTCCAGTAATTAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCAgtaagttcctatggttcatttgtactgggaagatattttattatctcatggcctagaacagttaaatatgacacttatttctggtacag

- - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - -  CATGGA