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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataatacacattttcaaatttttttgtctcaaacaatgcaggcgagctgtgtatctttgtattagagatagaagaagaggcaatcacttacaag...

Basic information

species Zea mays
transcript GRMZM2G086030_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086030_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 5'ss of exon 22
TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataatac----acattttcaaatttttttgtctcaaacaatgcaggcgagctgtgtatctttgtattagagatagaagaagaggcaatcacttacaag
|||||||||||| ||||||| ||||||||| || |||||||||||||| |||||||  ||||| ||  |||||||||||||||||||||||| |     || |||||||| || ||  | | |||  ||| || |        ||  |    | | || |  | |||  |  | |||| |      
TGTATCAGATCTACTTGACTACATAAGCCCGGATCAGGAAAGAAAAGAGAGGGATACACAAAGAAAGGGCAGGCGTGCAAAGgtgattataacatgcctactttttcaaaattattgttgttaaa--atgtagtcagaagagataagtgcacactggacagtggagacaattccatcagtattc--
















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|211017605|gb|FL188943.1|FL188943
EST:     ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG                         AATAATATCAGAGCTCATCACGGTGAATCAGTTGAAGAGAAGGAGAATTTT
genomic: ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTT
EST: gi|67035470|gb|CO464003.1|CO464003
EST:     ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG                         AATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTT
genomic: ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTT
EST: gi|31354896|gb|CD439253.1|CD439253
EST:     ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG                         AATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTT
genomic: ACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTT

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: 118

TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTTCAGCTTGTTTCAGGATCTCCTCTTGAAGCAAGCAAAGACAGTTTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTTCAGCTTGTTTCAGGATCTCCTCTTGAAGCAAGCAAAGACAGTTTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTTCAGCTTGTTTCAGGATCTCCTCTTGAAGCAAGCAAAGACAGTTTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 729

TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataa ... ttaattgcagAATAATATCAGAGCTCATCATGGTGAATCAGTTGAAGAGAAGGAGAATTTTCAGCTTGTTTCAGGATCTCCTCTTGAAGCAAGCAAAGACAGTTTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAGgtgattataatacacattttcaaatttttttgtctcaaacaatgcaggcgagctgtgtatctttgtattagagatagaagaagaggcaatcacttacaag

- - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaga