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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggagggagtatgatttaaagtagaaggttctaaataagttagataagtatgtctttttcagttaaagttggccattaactttgatcttgaaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG

Basic information

species Zea mays
transcript GRMZM2G094255_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g52710.3 (Oryza sativa), 3'ss of exon 2
-cggagggagtatgatttaaagtagaaggttctaaataagttagataagtatgtctttttcagttaaagttggccattaactttgatcttgaaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG
  | |     |    ||  | |||  ||  | || | | | |  |||| |||| || ||| ||| |||  |||||||||| | ||    |  ||||| |||||  ||||||| ||||| |||||||| || |  ||||| ||||  || ||||| || || ||||| ||||||||||| || ||||| |||||||||||||
ttgtatatgtttctcttgtaggtaccagtctttacacatgctgcataaatatg-ctcttttagtcaaatctggccattaattctgtgtctataacttacagCAACTGGCATCTCATGGGCTCTTTGACGTATGTGTTAAGGCAAAGGGTGACACTCACATCGATGACCATCACTCAAACGAAGACATCGCTTTGGCAATTG
















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|31355338|gb|CD439695.1|CD439695
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006666|gb|FL081503.1|FL081503
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|71309481|gb|DR791027.1|DR791027
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006668|gb|FL081505.1|FL081505
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTAC
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006664|gb|FL081501.1|FL081501
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006671|gb|FL081508.1|FL081508
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|50325237|gb|CO520363.1|CO520363
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006662|gb|FL081499.1|FL081499
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006669|gb|FL081506.1|FL081506
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|88757021|gb|DY541162.1|DY541162
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|91056439|gb|EB166857.1|EB166857
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|31611949|gb|CD568571.1|CD568571
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211003886|gb|FL081493.1|FL081493
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|149110134|gb|EE293952.2|EE293952
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|101397352|gb|EB820599.1|EB820599
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|211006657|gb|FL081494.1|FL081494
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         ---TTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGAT                         CAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC
genomic: GTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGAC

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: 81

GGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG


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

GGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 118

GGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 84

GGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGGGATACCGTTCTTGGATCACATGCTCGATgtgagtagtt ... aaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtatgtctttttcagttaaagttggccattaactttgatcttgaaacttgcagCAGTTGGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTG
                             attaacttt  TA-rich tract