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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctatatttaagccaaatttagatgctagtaacccaaatttgctgggactaaatgattttgttgttttgtgtatgttcttgaaaaacaaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG

Basic information

species Zea mays
transcript GRMZM5G860938_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860938_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g04940.1 (Oryza sativa), 3'ss of exon 8
----tttttctatatttaagccaaatttagatgctagtaacccaaatttgctgggactaaatgattttgttgttttgtgtatgttcttgaaaaacaaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG
    |    || |||  ||       |||| || |   | |    |     |   | |  |  | |      | || | | | ||  || |||  |   ||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| ||||| |||
agtctcaaactgtatgaaatattcccttaggtgtttacatcatgcagca--taacaatccactaatccaccatcttat-tgtcttgctgtaaa-tattttgtagGAAAGACTTATGTCTAAAGGCCAACAAATAAGTGAGAATTTCTATGTCAGAGGGGATGGCACG
















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|71449026|gb|DR830076.1|DR830076
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAG                         GAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
EST: gi|50330790|gb|CO525916.1|CO525916
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAG                         GAAAGACTGATGTCNAAGGGCCAACAAATAAGTGAGAACTTCTATGTCA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCA
EST: gi|148964289|gb|EE015484.2|EE015484
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAG                         GAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
EST: gi|32930653|gb|CF035465.1|CF035465
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTTGGTGATCTTGCACAG                         GAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
EST: gi|89760611|gb|DY688948.1|DY688948
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAG                         GAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
EST: gi|74241391|gb|DT649305.1|DT649305
EST:     ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAG                         GAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA
genomic: ATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGA

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), 33 (downstream exon)
Score: 187

CATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 180

CATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 158

CATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 113

CATGGTGGCCGTGTTCTTTTTCGGGACTATGCCTTCGGTGACCTTGCACAGgttgaatttc ... caaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgggactaaatgattttgttgttttgtgtatgttcttgaaaaacaaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG
     gactaaa  putative branch site (score: 113)
        taaatgattttgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctatatttaagccaaatttagatgctagtaacccaaatttgctgggactaaatgattttgttgttttgtgtatgttcttgaaaaacaaactgtagGAAAGACTGATGTCAAAGGGCCAACAAATAAGTGAGAACTTCTATGTCAGAGGTGATGGTACG

- - - - - - - - - - - - -gatgcta
- - - - - - - - - - - - - - - - - aacccaa
- - - - - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtatg