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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcaccttttttgattattgcaacttcgtttgatattttgtgtgcctttttatcatgggtcatatgacgtttaatcttagtaacttgttacttgc...

Basic information

species Zea mays
transcript GRMZM2G178227_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 5'ss of exon 3
TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtatt------gtcaccttttttgattattgcaacttcg--tttgatattttgtgtgcctttttatcatgggtcatatgacgtttaatcttagtaacttgttacttgc
||| || ||| |||| || || |||||||| || |||||| |||||||||| |  |||||||| |||||||||||||| | ||||||||||||||| ||||||||      || || ||||||  |  ||| ||  | |  |||| |  | |  || |   |  |||||     |||  | |||||| || |||| | ||| |     
TGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTGGAGAGgtatttaacttgtaacatttttt--tccttgtaatcttgcctttgtttatcttcgtactggtacatcataatgtataccatgtttaaactgagta-cctgtga-----
















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|60393978|gb|DN226848.1|DN226848
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|31353537|gb|CD437894.1|CD437894
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|78087329|gb|DV515722.1|DV515722
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|211324079|gb|FL420998.1|FL420998
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTT
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTT
EST: gi|76285477|gb|DV025045.1|DV025045
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|211048309|gb|FL397306.1|FL397306
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTAT
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTAT
EST: gi|211186071|gb|FL219845.1|FL219845
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA

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: 691

TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 608

TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 376

TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcaccttttttgattattgcaacttcgtttgatattttgtgtgcctttttatcatgggtcatatgacgtttaatcttagtaacttgttacttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA