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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcccaacccccgccttcctgtttctctgtccgttgctagggtttgcgccgctccgggtaacggatatgactgctgtgttgcataggggtcacg...

Basic information

species Zea mays
transcript GRMZM2G368908_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 1
CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcccaacccccgccttcctgtttctctgtccgttgctagggtttgcgccgctccgggt--aacggatatg-actgctgtgttgcat-aggggtcacg-----
||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||| ||   ||| |   |   ||||   ||||      | || |  || ||  || |  |  || |||| ||  |||||   | || | |||| || ||     
CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTGCTCCTCGGCACCTCCTCCCGCGGTTCCGTCGATGTCACCAACTCCTACGCCGgtaaaccttcc---cccagtactagggtttgcgtgtc------tcggatcagcccccttctgtttccaagggatctgcgctgctagttcgccttagggttcgcgcaact

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 1
-CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcccaacccccgccttcctgtttctctgtccgttgctagggtttgcgccgctccgggtaacggatatgactgctgtgttgcataggggtcacg--
  |||||||| | ||||||   ||||| ||||||||||||||||||||| | |||||| |||||| |   ||| |||||||||| ||||||  |||||| ||||    ||  | | | |    || | ||||| | |||  | ||  ||          |||   |  |   | ||  |  | | |  |       | |    
CAACTACAACAGAGTCGCCAAAGACACTCGCAAGCGCGTCGTCGGCGTCTTGCTCGGCTCCTCCTTCAAAGGCACCGTCGACGTTACCAACAGCTACGCCggtacggatctgatctctc--tctcttttttctttctccaatacttagggcatttttattcccttttccctttttgttt-ttctctctctctaaaattagatc

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 1
CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcccaacccccgccttcctgtttctctgtccgttgct-agggtttgcgccgctccgggtaacggatatgactgctgtgttgcataggggtcacg--
 |||||||| | ||||||   ||||| ||||||||||||||||||||| | |||||| |||||| |   ||| |||||||||||||||||  |||||| ||||    ||  | | | | | ||    ||||| | |||  | || |||| |||      |              |   || |   || |   |   | ||   
AACTACAACAGAGTCGCCAAAGACACTCGCAAGCGCGTCGTCGGCGTCTTGCTCGGCTCCTCCTTCAAAGGCACCGTCGACGTCACCAACAGCTACGCCGgtacggatctgatctctctctttt---tttctttctccaatacttagggcttgttttatttattcccttttcactttttgtttcttttctctgaaattacagt

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|149042715|gb|EE047230.2|EE047230
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|88755238|gb|DY539379.1|DY539379
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211156546|gb|FL393678.1|FL393678
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211522109|gb|FL427322.1|FL427322
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211358110|gb|FL397036.1|FL397036
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|71301807|gb|DR786975.1|DR786975
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211163165|gb|FL410935.1|FL410935
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|15208970|gb|BI430854.1|BI430854
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211365903|gb|FL387058.1|FL387058
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGAC
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGAC
EST: gi|211397663|gb|FL378752.1|FL378752
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGAACACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|20507024|gb|BQ279450.1|BQ279450
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGCTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|148973687|gb|EE024808.2|EE024808
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|18964870|gb|BM661257.1|BM661257
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|22490364|gb|BU050287.1|BU050287
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|26456618|gb|CA828201.1|CA828201
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211186910|gb|FL380819.1|FL380819
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211023018|gb|FL425563.1|FL425563
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211024429|gb|FL373968.1|FL373968
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
EST: gi|211499366|gb|FL394921.1|FL394921
EST:     CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGG                         TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA
genomic: CCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACA

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: 109

CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 52

CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcc ... ttttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTACAACCGCGTCGCCCGCGACACCCGCAAGCGCGTCGTCGGCGTCCTCCTCGGCACCTCCTCCCGCGGCTCCGTCGACGTCACCAACTCCTACGCGGgtaaacctcccaacccccgccttcctgtttctctgtccgttgctagggtttgcgccgctccgggtaacggatatgactgctgtgttgcataggggtcacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgctcc