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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcaccatatatatttacttgctcataggaacaatttctagcgattttcataagtaggctattttctctgtactatcaatgtatgatcatcttctct...

Basic information

species Zea mays
transcript GRMZM2G142984_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142984_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 4
GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcaccatatatatttact-tgctc-ataggaaca--atttctagcgattttcataagtag---gctattttctctgtactatcaatgtatgatcatcttctct
||| ||||||| ||||||||||||||| |||||||||||||||||||||||||||||| |||||  || |  | ||| | ||||   ||   || ||  | |  || |||  ||    | || |||||||||  | |  |||||  || ||       
GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAGgtaatcagcatatgcatgtggtgtgcactatagtggcatgcttactgactaaatttatagttaactcggtactttctctgttgtttacatgta-aattatt------
















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|67014473|gb|CO443222.1|CO443222
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGAAGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|149070923|gb|EE159330.2|EE159330
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|149000223|gb|EE037369.2|EE037369
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|89758395|gb|DY687589.1|DY687589
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|149102743|gb|EE188274.2|EE188274
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|67016231|gb|CO444980.1|CO444980
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGNNNNNNNGAAGAC
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAA-GATGAC
EST: gi|148965239|gb|EC906094.2|EC906094
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|211448014|gb|FL403750.1|FL403750
EST:     CTTTGTATTTTCAGTATGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCACGAGCAGGAAGGACAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|211115805|gb|FL350299.1|FL350299
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGAAGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
EST: gi|148995982|gb|EE035233.2|EE035233
EST:     CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG                         ATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA
genomic: CTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACA

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), 47 (downstream exon)
Score: 246

GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 476

GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 476

GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 495

GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcacca ... ttgtgtgcagATTGCTTATTCTCTGATAGAAGAGCAGGAGCAGGAAGGAAAAAAGATGACATCTGATGATTACAATTACATATCTTTTGTCAGCCTTCTTGCTGATAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAGgtaatcaccatatatatttacttgctcataggaacaatttctagcgattttcataagtaggctattttctctgtactatcaatgtatgatcatcttctct

- - - - - - - - - - - - - - - - - - - GATGGA