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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcccacagtaggttcttaatagattataattattagtatatgtataattcaatcacctgtataaattaaattttcacctggctccataatgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT

Basic information

species Zea mays
transcript GRMZM2G069758_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 10
--tgcccacagtaggttcttaatagattataattattagtatatgtataattcaat-cacctgtataaattaaattttcacctggctccataatgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
  ||  | |||   | |||| ||||   ||   ||| ||||  |   | ||  | | |     | |    ||||||||  ||||  | | ||||||| ||||||| ||||||||||| |||||||| || ||||||||||||||||||
tctgtgc-cagcttggtcttgatag--cattgctatcagtaactacttcatcgagtactttcatgttgcataaattttatcctgaattcgtaatgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
















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|18166331|gb|BM336170.1|BM336170
EST:     GATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: GATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|33097992|gb|CF057952.1|CF057952
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|86471052|gb|DY237422.1|DY237422
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTA
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTA
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGGCAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG                         GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
genomic: AGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT

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), 45 (downstream exon)
Score: 54

GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 212

GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 252

GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 99

GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccat ... tgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattcaatcacctgtataaattaaattttcacctggctccataatgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT
             tgtataaattaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcccacagtaggttcttaatagattataattattagtatatgtataattcaatcacctgtataaattaaattttcacctggctccataatgctatgcagGGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-gcccaca
- - - - - - - - - - - - - - - - - - - atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - cacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccat