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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgcatggtttaacattaataatttaatatgcattactaaagattatgggatgaagcctaaattcatttgatttgttttacacaccatttttagtttaccagaaccttgacagttcaattttgcag

Basic information

species Zea mays
transcript GRMZM2G044348_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044348_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 6
GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgcatggtttaacattaataatttaatatgcattactaaagattatgggatgaagcctaaattcatttgatttgttttacacaccatttttagtttaccagaaccttgacagttcaattttgcag
| |  ||||   ||| |||||    || |||||    |||||||| |   ||||||||||||| ||||| ||| |  ||||  | ||||||||||||||||||||||    |   |  | || |||   ||| | |   ||   ||      | |    || |   |||| |||  || | ||||| ||   |||||| || | |||   || |                  
GGTCGTTGCTGGAATCCCTGGGACATTTTTTTGTGCCTGGTATGCTTTGCAGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAGgtttgttgcttttcctatatataaatg--ttatttttttttgtcaa------ttgagccaatc---aattgatt--atgttttttatactaaatttttggtat-ccatttccat------------------
















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|71435689|gb|DR816739.1|DR816739
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAAATGCTGTCATTGGGATCATTTAAA
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAA
EST: gi|148948442|gb|EC893960.2|EC893960
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGG
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGG
EST: gi|148948218|gb|EC893734.2|EC893734
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGT
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGT
EST: gi|91875915|gb|EB405872.1|EB405872
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGGAT-GAGATGCTGTC
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGG-ATTGAGATGCTGTC
EST: gi|149097124|gb|EE182936.2|EE182936
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCC
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCC
EST: gi|149001048|gb|EE038297.2|EE038297
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCAT
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCAT
EST: gi|149100817|gb|EE186911.2|EE186911
EST:     AGAAGCATTGGCTTGCNAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG
EST: gi|78088713|gb|DV517106.1|DV517106
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATT
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATT
EST: gi|148943973|gb|EC889054.2|EC889054
EST:     AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG

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: 263

GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... aattttgcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTATTGCCTCAATACCTGGATTTTTCTTTTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAACAATGTCCTGGGATTGGCTTTCTGTATTCAGgtttgtttgcatggtttaacattaataatttaatatgcattactaaagattatgggatgaagcctaaattcatttgatttgttttacacaccatttttagtttaccagaaccttgacagttcaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC