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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacgtaggatcatattgcttaaatctagttgctaattttagtttgacaaatgatgtttgggtcatcctgtttcacatattgaactttatattattagtaatatttctgttgcttatttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA

Basic information

species Zea mays
transcript GRMZM5G836588_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 4
gtacacgtaggatcatattgcttaaatctagttgctaattttagtttgacaaatgatgtttgggtcatcctgttt-cac-----atattgaac---tttatattattagtaatatttct------gttgcttatttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA
||||  |||  ||| | | | | ||||    |   ||||      || |||  | ||   | | | | | ||| | |||      | |||||       ||  | |||||||| | | |      ||   ||||||||||||||| |||||||| || || ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||
gtacttgtataatcgtgtggatcaaat----tctttaatccgtagttaaca--tcattcctagtttaacatgtatgcactgctggttttgaatcaacgcatgctgttagtaatttcttttaattggtcttttatttcattagCATTGCAATGGGCTGCATTTACACGGAAGCTAAAAACTACCCTCGTGAGCCAGCTGCCCATGTGGCGATAA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacacgtaggatcatattgcttaaatctagttgctaattttagtttgacaaatgatgtttgggtcatcctgtttcacatattgaactttatattattagtaatatttctgt-tgcttatttcatt--agCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA
      ||    | | ||| ||    | |  ||  |  |||        |||||  | ||   ||  |    ||  |  | |  | | | |  | |  |     ||||  || ||| ||   ||||  || |||||  |||| ||||||||||||||||| |||||||| || || ||||||||||||||||| || ||||
--gtgtgtgaagtgaaatt-ctagttttttcttatttttttgcaacaatcaaattctattgtagttttgtgatt--atctttgtatcctgaactcaagaacttgattttggtctgcatacaacattgcagTATCGCTCTGGGCTGTATATACACAGAAGCCAAAAACTATCCCCGAGAACCAGCTGCTCATGTTGCCATAA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtacacgtaggatcatattgcttaaatctagttgctaattttagtttgacaaatgatgtttgggtcatcctgtttcacatattgaactttat--attattagtaatat--ttctgttgcttatttcat---tagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA
                 ||| ||      || || ||  || | ||         ||   | | |||||   | | || | ||    ||| |  || |   | ||| |  ||   |||    |||       ||||| || ||||| || ||||| ||||| |||||||| || ||||| ||||||||||| |||||||| ||||
----------------gttggttgctatcagatgttacattcatttctttcttgtatagattgttcatcacttgttacctttttttttttcttaatgaacgggaatttagtttaattgacatttttggatgcagCATTGCTATGGGCTGCATATATACAGAGGCTAAAAATTATCCTCGGGAACCAGCTGCACATGTGGCTATAA

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|211381535|gb|FL250722.1|FL250722
EST:     CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAG                         CATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
genomic: CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
EST: gi|76286118|gb|DV025686.1|DV025686
EST:     CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAG                         CATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
genomic: CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
EST: gi|93016568|gb|EB642088.1|EB642088
EST:     CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAG                         CATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
genomic: CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
EST: gi|211381540|gb|FL250727.1|FL250727
EST:     CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCT-GAAAG                         CATCGCAATGGG
genomic: CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGG
EST: gi|148931777|gb|EC875053.2|EC875053
EST:     CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAG                         CATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC
genomic: CACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACC

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), 47 (downstream exon)
Score: 77

GCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 45

GCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GCCCCAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGTCACTGCTATCGGTCCTGCTTGGAACTGCTCATTGAGAATGGTCTTGAAAGgtacacgtag ... atttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacatattgaactttatattattagtaatatttctgttgcttatttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA
                                          cttatttc  CT-rich tract
      atattgaactttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacgtaggatcatattgcttaaatctagttgctaattttagtttgacaaatgatgtttgggtcatcctgtttcacatattgaactttatattattagtaatatttctgttgcttatttcattagCATCGCAATGGGTTGTATATACACAGAAGCTAAAAACTACCCTCGTGAACCAGCTGCTCATGTGGCAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT