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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttatttctggtacag

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 14
GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttatttctggtacag
||||||||| |||||||| ||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||  |     ||| | |  ||| |     |||   | | |  |   | || || |||  |      | |||||   | |||
GCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCCTGGATGAATGATTTTATCCGCCAgtaagttctgaccaggcatatct--tggga-----ctaaagttttg-gcaagaaaggagataatgaaaat-ttcatttcgcatgcag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 14
GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttatttctggtacag
||||||||| |||||||| ||||||||||||||||||| ||||| ||||||| ||||||||| ||||||||||||   ||||  ||| | | |||| |   |   ||||| | | ||   |  |   |||        | |||||||| || |||
GCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCGTGGATGAGTGATTTTATCCGCCAgtaagttgtcatggagcatgtatcctgggat--tagaattatgttg-acaagaaggtgattatggtaa--atttatttctcgtgcag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G00590.1 (Glycine max), 5'ss of exon 14
GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttat-ttctggtacag
||||| |||||||||||  | || || ||||| |||||||| ||||||   ||||||| |||||||||||||||  | ||  || | | ||| |       ||  ||| | |    | ||  |   || | |  ||  | ||   || | || |||
GCTGCTGCTTTGGCTCTCCGTAAAGTTCCTCAATGTAACAGTTCATGGGCAAATGATTATATTCGCCAgtaagtctacattttttaat-gtagtattgccatcaaatt-tgtgaatcactttaattgtaacatttgttaatttcatttttgtgcag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 14
GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttatttctggtacag
||||| |||||||||||  | || || ||||| |||||||| ||||||   ||||||| |||||||||||||||  | |   || | | ||| |       ||  ||| | |    |  |  |   || | |  |   | ||  || | || |||
GCTGCTGCTTTGGCTCTCCGTAAAGTTCCTCAATGTAACAGTTCATGGGCAAATGATTATATTCGCCAgtaagtcaacaatttttaat-gtagtattgccatcaaatt-tgtgaatcattttaattgtaacattttttattttgtttttgtgcag

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|20802763|gb|BQ293813.1|BQ293813
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACA
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACA
EST: gi|71329666|gb|DR801555.1|DR801555
EST:     CATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: CATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|26456540|gb|CA828123.1|CA828123
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAAACATCAACGTGGCTGTGCAGACTGAACACGGATTGT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTG-AACATCAACGTGGCTGTGCAGACTGAACACGGATTGT
EST: gi|32932090|gb|CF036902.1|CF036902
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|32933945|gb|CF038757.1|CF038757
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|21809700|gb|BQ668018.1|BQ668018
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATT
EST: gi|32930018|gb|CF034830.1|CF034830
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|32934396|gb|CF039208.1|CF039208
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|22472155|gb|BU036635.1|BU036635
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTT
EST: gi|20208122|gb|BQ134196.1|BQ134196
EST:     AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCA                         ATATCACAATGTGAACATCAAC
genomic: AGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAAC

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: 214

GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 306

GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 516

GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcat ... tctggtacagATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGCTTTGGCTCTTAGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGCCAgtaagttcatatggttcatttgtactggaaaggtcctattatctcgtaccctagagcagttaaaaatggcacttatttctggtacag

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