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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagctgcagcaagctgcaacaccagtgatgatgtgtagaaaaagctgtaattatcaccagccaggaactttagttaattgctgtgatgattttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA

Basic information

species Zea mays
transcript GRMZM2G134862_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134862_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g30640.1 (Oryza sativa), 3'ss of exon 5
aaagctgcagcaagctgcaacaccagtgatgatgtg-tagaaaaagctgtaat--tatcaccagccaggaactttagttaattgctgtgatg--attttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA
       |  ||  |   ||   | ||  |  | |    |||    || |  |  | | ||           | ||||  ||  |||| |||  ||||| ||||||| |||| |||||| || || ||||||||||| |||||||||||||| | || ||| |||   ||  |||| || ||||||||||| |||||||||||||
-----aacttcacacgataatgtctgtttttttttaactgaatgttctattgttctgttacattttgattgatgtagtacataactgtaatgctattttgtgcagCCGAGATATGTAGTGAACCGTGTCACTGCTGGAGACTATGACTGTCCAAGAAAGGTGTTGTCATTTCTGACAGACCTTCATGCTTCATTTAGGATGCTGA
















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|88748677|gb|DY532818.1|DY532818
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|211145650|gb|FL480705.1|FL480705
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|78109960|gb|DV528375.1|DV528375
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|88747276|gb|DY531417.1|DY531417
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|6994090|gb|AW453304.1|AW453304
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCTG-CTATGACTGTCCTAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGC-GACTATGACTGTCCTAA
EST: gi|76285577|gb|DV025145.1|DV025145
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTNAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|71448432|gb|DR829482.1|DR829482
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|74240450|gb|DT648364.1|DT648364
EST:     TCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: TCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|86470223|gb|DY236593.1|DY236593
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|60340983|gb|DN207956.1|DN207956
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCTG-CTATGACTGTCCTAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGC-GACTATGACTGTCCTAA
EST: gi|194717187|gb|FK934340.1|FK934340
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|93016579|gb|EB642099.1|EB642099
EST:     GACTGTGCTTCATGTCCAATGAATTT                         CCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA
EST: gi|211468306|gb|FL243202.1|FL243202
EST:     GACTGTGCTTCATGTTCAATGAATTT                         CCTAGATTTGTAGTAAATCGCATCACTGCTGGCGACTATGACTGTCCTAAA
genomic: GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 133

GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 53

GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 41

GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 64

GACTGTGCTTCATGTCCAATGAATTTgtaagttcat ... ttttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaattatcaccagccaggaactttagttaattgctgtgatgattttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA
                           agttaat  putative branch site (score: 64)
                                             ttttttgc  putative PPT
                     aactttagttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagctgcagcaagctgcaacaccagtgatgatgtgtagaaaaagctgtaattatcaccagccaggaactttagttaattgctgtgatgattttttgcagCCTAGATTTGTAGTAAATCGCGTCACTGCTGGCGACTATGACTGTCCTAAAAGGGTTTTGGGCTTCTTGACCGATCTTCATGCTTCGTTTAGGATGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- -gctgcag
- - - - - - -gctgcaa
- - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - gctgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgctg