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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcatcttagatttacatgatgtaatgggttttataattgacatttttcttatatctgatgctttcaccaccctattgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG

Basic information

species Zea mays
transcript GRMZM2G100913_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os08g42740.2 (Oryza sativa), 3'ss of exon 12
gtctgtcatcttagattta-catgatgtaatgggt--tttataattgacatttttcttatatctgatgctttcaccaccctattg----tacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG
|| ||  ||| || || |  |||||   ||  |    |  ||| |  ||| ||  | |   |||||||| | |||||  | | |     ||  ||||||||| ||||||||||| ||  | ||||||||||||||||||||||| |||||||| || ||| ||||||| |||||||| ||||| |||||||
gtttgatatcataaatatgtcatgacccaaatgacactccatactatacaattcacctgcgtctgatgcatgcaccattccactatgtctatttcagATTATTGAATGCAGGCGGGTACTCAAATGGACATATGCTTATGGCTATTATCTGGACGACAAGGTCAAGAGCGAATTTTTCGAGTACCTGCAAG

upper sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------------------------------------------gtctgtcatcttagatttacatgatgtaatgggttttataattgacatttttcttatatctgatgctttc--accaccctattgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCT------GGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG
                                                                                                || ||  |  ||   ||       | |  | ||    || |||  |     ||  | |    || | ||   | |    | ||||    |||||| |||||||| |||| || ||||| ||||||||||||||||| || ||  |      | ||||  | |  || ||  |||| ||||| ||   |||||
gttaatacactttgtgcgtggacatgttatttttgcgcttgctggatatcctttgtcttaattacgttatttattgcatataatgcggagtatggagtgtggaacattcatttggagcatttttctcggaagcatcattatccacaatcacaaactgtattccttttaatcgtttttttgttgtgcagATTGTAGAATGCCGGCGTGTATTGAAGTGGACATATGCTTATGGATATTACTTACCTGAGAATGAGCACACGAAAAGACAATTCTTTGAATACTCGCAAG
















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|87156257|gb|DY401046.1|DY401046
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|31355723|gb|CD440080.1|CD440080
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|31909111|gb|CD650755.1|CD650755
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|67010842|gb|CO439591.1|CO439591
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|26559055|gb|CA831290.1|CA831290
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|31364271|gb|CD448626.1|CD448626
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|29543802|gb|CB604182.1|CB604182
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|211250423|gb|FL206024.1|FL206024
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|213179909|gb|FM186344.1|FM186344
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
EST: gi|22549188|gb|BU101389.1|BU101389
EST:     TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAG                         ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT
genomic: TCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTAT

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: 564

ATTGCAAATTTAACTGACATTTTCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 338

ATTGCAAATTTAACTGACATTTTCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 418

ATTGCAAATTTAACTGACATTTTCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 404

ATTGCAAATTTAACTGACATTTTCGGGATACCAGAGACCCAGCTTAAGTTCATAATCGAAGCTTGGTCACAGgtctgtcatc ... tgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataattgacatttttcttatatctgatgctttcaccaccctattgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG
                                       ccctatt  CT-rich tract
         acatttttcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcatcttagatttacatgatgtaatgggttttataattgacatttttcttatatctgatgctttcaccaccctattgtacatcagATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA