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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatctccctaaactattgtactttggtattttgtttacaatcaactcattaattgcttggataattccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 10
gtatgtcatc---tccctaaactattgtactttggtattttgtttacaatcaactcat-taattgcttggataattccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG
|||| ||| |   ||   || || ||||  |||  | |||| | | |||||| || |  || |||| || ||||||| ||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||
gtatatcaccgcatcttaaatctgttgtg-tttattcttttatatgcaatcagcttagatagttgcctgaataattctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG
















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|60343993|gb|DN210966.1|DN210966
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|32930219|gb|CF035031.1|CF035031
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|211238345|gb|FL044423.1|FL044423
EST:     GCATTGGAGCGAATGGNAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCCGACCC-AGATGACCGCCCTGGGCCACCAATCA
genomic: GCATTGGAGCGAATGG-AACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCA-ACCCCAGATGACCGCCCTGGGCCACCAATCA
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|32932155|gb|CF036967.1|CF036967
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|32932545|gb|CF037357.1|CF037357
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCAT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCAT
EST: gi|32848242|gb|CD987923.1|CD987923
EST:     GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGA                         CTATAAATTTGAATTT
genomic: GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTT

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: 290

GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc ... ttccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttggtattttgtttacaatcaactcattaattgcttggataattccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG
                           cattaat  putative branch site (score: 226)
                                             ttccttgc  putative PPT
       tattttgtttacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcatctccctaaactattgtactttggtattttgtttacaatcaactcattaattgcttggataattccttgcagCTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT