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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaattttgtaagaccatacttgggataaagattgaatctattctcttctcttacaaaagttataacataacattttcacatttcttccctgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA

Basic information

species Zea mays
transcript GRMZM2G461145_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 8
acaattttgtaagaccatacttgggataaa---gattgaatct--attctcttctcttacaaaagttataacataacattttcacatttcttccctgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA
    |      | | |||  ||    ||||   ||   ||  |  |||| | | ||||    |  || | | ||    |||   |  |||| |  ||||| ||||||   || |||||||||||||||||||||||||| ||||||||  | ||||| ||||| ||||||||||| || ||| |  
----tgcaaggaaaacatgttttacttaaacctgacccaacttggattcacatttcttgtcgatcttctga-atgtgttttaagctgttctcctgtgttacacagTTCATTGTAGGAATCCACAAACTGAGTCTTTTCTGCAGCTTCTAAATCTCCCGTATCTTCTGGACTCATCAAATTCTTATG
















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|211425655|gb|FL472964.1|FL472964
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|5525743|gb|AI861636.1|AI861636
EST:     TGCACCATCTTTCAATCCTTCCAGTNCAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCCCAAACTGAGTCTTTTCATCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|67037524|gb|CO464338.1|CO464338
EST:     CACCATCTTTTTCA-TCCTTCCAGTACCACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCCACAA-CTGAGTCTTTTCT-CAGCT-CTGGAACTC
genomic: CACCATCTTT--CAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCC-ACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTC
EST: gi|211437922|gb|FL449193.1|FL449193
EST:     AGCCCCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|211383644|gb|FL455006.1|FL455006
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|32863094|gb|CF002776.1|CF002776
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|83279349|gb|DV943357.1|DV943357
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCNNNNNNNCAGCTTTTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|17931921|gb|BM268881.1|BM268881
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
EST: gi|17931886|gb|BM268846.1|BM268846
EST:     TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAG                         TTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC
genomic: TGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCC

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: 46 (upstream exon), 43 (downstream exon)
Score: 27

AGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 28

AGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA


Block sizes: 27 (upstream exon), 43 (downstream exon)
Score: 10

AGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA


Block sizes: 40 (upstream exon), 43 (downstream exon)
Score: 9

AGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCTTTCAATCCTTCCAGTACAACATCTAAACAGTCCATAACAGgtaagtttga ... tgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcttacaaaagttataacataacattttcacatttcttccctgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA
                            ttttcacatttcttcc  CT-rich tract
          aaaagttataacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaattttgtaagaccatacttgggataaagattgaatctattctcttctcttacaaaagttataacataacattttcacatttcttccctgttatacagTTTGCTGCAGGAATCCACAAACTGAGTCTTTTCTTCAGCTTCTGGAACTCCCATATCTGCTGGACTCATCTAAATCTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - ccatact
- - - - - - - - - - - - gataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - tacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataa