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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattggtatattctaaatgccaggttgctgttttgtatttgtaatgtttttggtattgctgcctgagtgagaaccatatattccttattgttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 7
cattggtatattctaaatgccaggttg-ctgttttgtatttgtaatgtttttg-gtattgctgcctgagtgagaaccatatattccttattgttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA
     | || || |  |      | || ||   || | ||  || | | |  |  || || |   | |   | || ||| |   |  |  |  |   ||||||||||||| ||| ||||||||||| || ||| ||||||| || || ||||| |||||||||||||| ||||| || ||||||||||| ||||||||||||
--cctgaattttattgacaaagtgatgtctagattatgttattactttctaagtatactggtattttatctaaaagcattttggcaattctaatacttgtagGAAAGAACAAGTTTGGCCAGAATTGGACCAACTGCTCCGTGATGAAGATGATACAACTGGTGCATCCACTCCTTACACTGCTGCTATACCTGAATACAGA
















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|148941319|gb|EC886225.2|EC886225
EST:     GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATG                         GAAAGAACTAG
genomic: GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAG
EST: gi|21809491|gb|BQ667809.1|BQ667809
EST:     GTTGGCCTTGGAGACGATGATCAGCGCATTGAGGATGATTTCACTGCATG                         GAAAGAACTAGCGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGA
genomic: GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGA
EST: gi|211095653|gb|FK967022.1|FK967022
EST:     TTGGCCT-GGNAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATG                         GNAAAGA-CTAGTGTGGGCAGAATTATGATCA-TTGCTCCGCGACGAGAAT
genomic: TTGGCCTTGG-AGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagG-AAAGAACTAGTGTGGCCAGAATTA-GATCAATTGCTCCGCGACGAGGAT
EST: gi|148940766|gb|EC885587.2|EC885587
EST:     GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATG                         GAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGA
genomic: GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGA
EST: gi|148970820|gb|EE021584.2|EE021584
EST:     GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATG                         GAAAGAACTAGTG
genomic: GTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTG

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: 461

GTGGGAAACGTCTTGTTCCTGTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 950

GTGGGAAACGTCTTGTTCCTGTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 773

GTGGGAAACGTCTTGTTCCTGTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1131

GTGGGAAACGTCTTGTTCCTGTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATGgtacaaaagc ... ttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttggtattgctgcctgagtgagaaccatatattccttattgttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA
                                   ttccttattgttttct  CT-rich tract
                              atatattccttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattggtatattctaaatgccaggttgctgttttgtatttgtaatgtttttggtattgctgcctgagtgagaaccatatattccttattgttttctgtagGAAAGAACTAGTGTGGCCAGAATTAGATCAATTGCTCCGCGACGAGGATGACACAACTGGTGCATCGACTCCATATACTGCTGCTATTCCTGAATACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - -aatgcca
- - - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgc