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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgattctcttgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacag

Basic information

species Zea mays
transcript GRMZM2G178958_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178958_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 5'ss of exon 2
GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgattctcttgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacag
|||||| | ||||||||||||||||| || || ||| |||| ||     |||||||||||||||| || |||||||||||||| |||||| ||||||| |||| |   |  |||||   | ||||||||        || ||| ||  || |||  |||| ||| | ||||||||| ||| |     |||| ||  |||
GCCAAGTCTGCTCAAGCTAGCAGCGCGGCTATTGTTTTTGCTTCAGTGGGTGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcag
















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|211130401|gb|FL313022.1|FL313022
EST:     GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|148936677|gb|EC880805.2|EC880805
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|93012171|gb|EB637691.1|EB637691
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|32804459|gb|CD956695.1|CD956695
EST:     CCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: CCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|67042042|gb|CO468297.1|CO468297
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTACGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|32789139|gb|CD941375.1|CD941375
EST:     GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|32804579|gb|CD956815.1|CD956815
EST:     GATCCCGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|149111708|gb|EE190853.2|EE190853
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|211473206|gb|FL353033.1|FL353033
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|32804806|gb|CD957042.1|CD957042
EST:     GATCCGGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|148972721|gb|EE023682.2|EE023682
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|149026812|gb|EE046172.2|EE046172
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|32804417|gb|CD956653.1|CD956653
EST:     GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|76291680|gb|DV031248.1|DV031248
EST:     CTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: CTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|211018803|gb|FL351168.1|FL351168
EST:     TCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTTGCTTCTG                         GAACCGTGCTGGGGTTKTATGAGGACAGCAGATACAAGTCTGAATCGAAA
genomic: TCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAG-TTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAA
EST: gi|76013429|gb|DT940599.1|DT940599
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|71323796|gb|DR798569.1|DR798569
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|211347363|gb|FL343425.1|FL343425
EST:     GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: GATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|87153061|gb|DY397850.1|DY397850
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|211116579|gb|FL349398.1|FL349398
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|67023272|gb|CO452021.1|CO452021
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTACGAGGACAGCAGATACAAGTCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|71448100|gb|DR829150.1|DR829150
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
EST: gi|110519120|gb|EE023707.1|EE023707
EST:     TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTG                         GAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA
genomic: TGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAA

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: 248

GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTGGTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 558

GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTGGTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 560

GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTGGTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgatt ... tgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTGGTGCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAGGCCGCTCAAGCTAGCAGCGCTGCAATCGTTCTTGCCTCCCCCAGTGGGATCCAGGAAGAGTTCAAGCTGACTGCTGCAGCAGCAGTTGCTTCTGgtacttgattctcttgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG