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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcgaaggcaccatctgctgctattagcattttgttttcgaaatttatatccatttatttcggtatcttgtttttttatgctttatgcttcttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
---ggcgaaggcaccatctgctgctattag-cat----tttgttttcgaaatttatatccatttatttcggtatcttgtttttttatgctttatgcttcttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT
   |  | | ||     |  ||||| |||| |||    ||  |||   || ||| |  || |  ||||  | | ||| |||| | ||| ||       ||||||| ||| ||| |  |||||||| ||||| | |||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||| | || ||||| ||||| |
cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacc-tgaattttagcaccttattttctcatgatt-------cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT
















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|60338877|gb|DN205850.1|DN205850
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|71764040|gb|DR961977.1|DR961977
EST:     AGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: AGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|71764041|gb|DR961978.1|DR961978
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAATAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|7227784|gb|AW566425.1|AW566425
EST:     TTCCCCTAGTGTTATAGCATCTGCACAG                         GGTTTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: TTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|166612126|gb|EG110687.1|EG110687
EST:     AGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: AGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|7238117|gb|AW573339.1|AW573339
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|60400196|gb|DN233003.1|DN233003
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|148966756|gb|EE017836.2|EE017836
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|148958743|gb|EC905020.2|EC905020
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|32934959|gb|CF039771.1|CF039771
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|32931620|gb|CF036432.1|CF036432
EST:     CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
EST: gi|60344484|gb|DN211457.1|DN211457
EST:     CCTAGTGTTATAGCATCTGCACAG                         GGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA
genomic: CCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGA

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: 183

CCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCCCTCAGAACAGAATCCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

CCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCCCTCAGAACAGAATCCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

CCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCCCTCAGAACAGAATCCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCCCTCAGAACAGAATCCAGCATTTATAACCCAACTACTTCCCCTAGTGTTATAGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatccatttatttcggtatcttgtttttttatgctttatgcttcttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT
                                   ctttatgcttctttt  CT-rich tract
                  tatcttgtttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcgaaggcaccatctgctgctattagcattttgttttcgaaatttatatccatttatttcggtatcttgtttttttatgctttatgcttcttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT

- - - ggcacca
- - - - - - -tctgctg
- - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctt