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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatacatatcttttctcgttatcctctaaatattttcctataataagtggtatttagtttgtccatagtccatacatctgacaaagtttaatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA

Basic information

species Zea mays
transcript GRMZM5G824600_T02
intron # 4
splice site 3'
intron type U2

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|148969452|gb|EE020260.2|EE020260
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211040047|gb|FL419088.1|FL419088
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211527705|gb|FL414610.1|FL414610
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|149055770|gb|EE156478.2|EE156478
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|148972824|gb|EE023810.2|EE023810
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|74034792|gb|DT535283.1|DT535283
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|149107259|gb|EE189142.2|EE189142
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|149001497|gb|EE038802.2|EE038802
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211392726|gb|FL395705.1|FL395705
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|148930859|gb|EC873272.2|EC873272
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|84980410|gb|DW530759.1|DW530759
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211288478|gb|FL412711.1|FL412711
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211271449|gb|FL402756.1|FL402756
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211087315|gb|FL378413.1|FL378413
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|148971977|gb|EE022778.2|EE022778
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|31355494|gb|CD439851.1|CD439851
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|31355865|gb|CD440222.1|CD440222
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|211356389|gb|FL426375.1|FL426375
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|149103654|gb|EE289058.2|EE289058
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTG
EST: gi|20811111|gb|BQ295589.1|BQ295589
EST:     ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTG                         GTCTTGGAGCG
genomic: ACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCG

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: 280

TTCAGCCAGTACACTGTGGTGCATGATGTCAGTGTTGCAAAGATCAACCCACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

TTCAGCCAGTACACTGTGGTGCATGATGTCAGTGTTGCAAAGATCAACCCACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 229

TTCAGCCAGTACACTGTGGTGCATGATGTCAGTGTTGCAAAGATCAACCCACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

TTCAGCCAGTACACTGTGGTGCATGATGTCAGTGTTGCAAAGATCAACCCACAGGCACCCTTAGATAAAGTCTGCCTGCTCGGTTGTGGTGTTCCTACTGgtatgttctt ... aatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtggtatttagtttgtccatagtccatacatctgacaaagtttaatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA
      tatttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatacatatcttttctcgttatcctctaaatattttcctataataagtggtatttagtttgtccatagtccatacatctgacaaagtttaatcatccagGTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccataca