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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaatcatttatactcttttggattctggaatgttctgctactctttttgttaaatctacagaagattggatgtgattttgatttttttgcag

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 4
GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaatcatttatactcttttggattctggaatgttctgctactctttttgttaaatctacagaagattggatgtgattttgatttttttgcag
 ||||| |||||||| |||||| | ||||| |||||||| ||||| ||||| |||||||| ||||||||||| || ||||||||||| |||   |||||||||| |   | ||| | | |    | | ||     |  || || || | |   |  |   | | ||  | ||||    || || |   || | |  ||
CATGGAATTTGTTCCTGAGTCACTGTATCGTGTGTTGAAGCATTATAGCAACATGAACCAAAGGATGCCACTTATATATGTCAAATTGTATGTTTACCAGgtaagatg-ttattgacaatacagttgcttact--actttttgttagtttccatagttg-tattcatgatattgatattgcttgtctgttctgtatag
















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|148952787|gb|EC898773.2|EC898773
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|148932530|gb|EC876330.2|EC876330
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|30031861|gb|CB833712.1|CB833712
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTT
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTT
EST: gi|76287882|gb|DV027450.1|DV027450
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     CATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: CATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|94476799|gb|EB705757.1|EB705757
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|149112787|gb|EE191425.2|EE191425
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|71430638|gb|DR811688.1|DR811688
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     CAAATTATATACCTACCAG                         ATATTTCGAGGCTTAG-CTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: CAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|91057059|gb|EB167477.1|EB167477
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|31351371|gb|CD435728.1|CD435728
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|71443964|gb|DR825014.1|DR825014
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|211298026|gb|FL233895.1|FL233895
EST:     CAAATTATATACCTACCAG                         ATATTTCGAGGCTTAG-CTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: CAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|148931707|gb|EC874917.2|EC874917
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
EST: gi|76922778|gb|DV169169.1|DV169169
EST:     ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAG                         ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG
genomic: ATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGG

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: 48 (upstream exon), 48 (downstream exon)
Score: 192

GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 121

GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaat ... ttttttgcagATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAGTTTGTTCCCGAGTCATTATATCGGGTGTTGAAACATTACAGCAATATGAACCAGAGGATGCCACTCATTTATGTCAAATTATATACCTACCAGgtaaaaaaatcatttatactcttttggattctggaatgttctgctactctttttgttaaatctacagaagattggatgtgattttgatttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG