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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatcctttcttatatttggctgggtaattctttgtttttcatgatacttgtcaaactttctatgtccttaacgaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG

Basic information

species Zea mays
transcript GRMZM2G105192_T03
intron # 7
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105192_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g01100.2 (Oryza sativa), 3'ss of exon 9
--------------atatcctttcttatatttggctgggtaattctttgtttttcatg---atacttgtcaaactttctatgtccttaacgaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG
               ||   ||  | ||||    ||    |   ||     | |  ||   ||   | |   |  |   ||  ||||||| |||||||||||||||||| |||||||||||| || |||||||||||||||| ||||| || |||||||| ||||||||  | |||||| |||||||||||||  |||||
acgaaattctcaaactacaattattcatatcatactttacatgactgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG
















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|91876287|gb|EB406244.1|EB406244
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|18173199|gb|BM348587.1|BM348587
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|16926851|gb|BM079919.1|BM079919
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|71446062|gb|DR827112.1|DR827112
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|18162838|gb|BM332677.1|BM332677
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|110220376|gb|EC902274.1|EC902274
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|110522223|gb|EE026407.1|EE026407
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|29544356|gb|CB604736.1|CB604736
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCNCTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|16922011|gb|BM075387.1|BM075387
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|113700925|gb|EE678429.1|EE678429
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|76288379|gb|DV027947.1|DV027947
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|18166790|gb|BM336629.1|BM336629
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|17929411|gb|BM266371.1|BM266371
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|17932564|gb|BM269524.1|BM269524
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|67015707|gb|CO444456.1|CO444456
EST:     CCACG-TGGCAAATCCAATAACCAA                         AT--GCATTA-CCATA-CCCCACT
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACT
EST: gi|71426676|gb|DR807726.1|DR807726
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
EST: gi|67019146|gb|CO447895.1|CO447895
EST:     CCACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC
genomic: CCACGGTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCC

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: 37 (upstream exon), 49 (downstream exon)
Score: 76

GTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG


Block sizes: 20 (upstream exon), 48 (downstream exon)
Score: 102

GTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 196

GTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 55

GTGGCAAATCCAATAACCAAatatcctttc ... gaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgtttttcatgatacttgtcaaactttctatgtccttaacgaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG
 gtccttaac  putative branch site 
       tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcctttcttatatttggctgggtaattctttgtttttcatgatacttgtcaaactttctatgtccttaacgaataatcacATATGCATTAACCATAACCCCACTGACTATGAGTTTGGAAGAGTTGCTTCCACCAAATCAACAGAAGTACTCAAACATAGTCATGCTTAGATCAGCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA