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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggatatgatcaaccatgatcgagtcctttgagatcaacccaaaaacttgtgctttctcccaactcgctgtttacttgccaattttctttcacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG

Basic information

species Zea mays
transcript GRMZM2G152757_T04
intron # 2
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|211140497|gb|FL400397.1|FL400397
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|50326445|gb|CO521571.1|CO521571
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211426998|gb|FL426768.1|FL426768
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|71435796|gb|DR816846.1|DR816846
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|93012264|gb|EB637784.1|EB637784
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|15208795|gb|BI430679.1|BI430679
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211027069|gb|FL381517.1|FL381517
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211217102|gb|FL383485.1|FL383485
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211084814|gb|FL392700.1|FL392700
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211131362|gb|FL428332.1|FL428332
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|91048113|gb|EB158531.1|EB158531
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTNAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|149037768|gb|EE155430.2|EE155430
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTTACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
EST: gi|211225357|gb|FL370946.1|FL370946
EST:     TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC
genomic: TGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGAC

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), 48 (downstream exon)
Score: 99

ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctg ... cacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtgctttctcccaactcgctgtttacttgccaattttctttcacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG
                                     ttttctttcac  CT-rich tract
                                   aattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggatatgatcaaccatgatcgagtcctttgagatcaacccaaaaacttgtgctttctcccaactcgctgtttacttgccaattttctttcacacattagGATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - catgatc
- - - - - - - - - - - - - - - - - - aacccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgc