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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttcaatatacacttaatggatgttgatgtttcattgtactcctctcttaaaacgacatctgggactgggatgcag

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 12
GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttcaatatacacttaatggatgttgatgtttcattgtactcctctcttaaaacgacatctggg-actgggatgcag--------
||||||||||| ||||||||||||||||| |||||||| ||||||  ||||||| ||| ||||||| |  | ||| |  ||||||||||| |||| || |||||   ||   | |  |||| |   | |||||  ||  ||| ||  |||    | |  |  ||||     | ||| |||  |        
GATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACCTGCTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt--tctctacttga--aaagttgaatttctattataacccttgtcttatccctcatccaaccattggaatggtggtctacag
















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|213179091|gb|FM180755.1|FM180755
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|60399462|gb|DN232274.1|DN232274
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|31664051|gb|CD573231.1|CD573231
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAAAACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|32944815|gb|CF049634.1|CF049634
EST:     CTTGCCAAGTGGACGACCGCCGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|5607686|gb|AI901353.1|AI901353
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|116824778|gb|EC868424.1|EC868424
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|12973361|gb|BG268442.1|BG268442
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|211466836|gb|FL414153.1|FL414153
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|60354737|gb|DN221710.1|DN221710
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|28983303|gb|BQ538545.2|BQ538545
EST:     TCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: TCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|60338924|gb|DN205897.1|DN205897
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|21626337|gb|BQ621258.1|BQ621258
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
EST: gi|78025807|gb|DV494194.1|DV494194
EST:     CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCG                         AACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA
genomic: CTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACA

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: 187

GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACATGAGGAAGTGAACCGGTGGTGGACGTGCTGGAGAGATCCCTGTTTCGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACATGAGGAAGTGAACCGGTGGTGGACGTGCTGGAGAGATCCCTGTTTCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACATGAGGAAGTGAACCGGTGGTGGACGTGCTGGAGAGATCCCTGTTTCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttc ... tgggatgcagAACTCGAAGGGCTCCCAATCGAGCTTGTCCATCGGATCGTTCCTGAACACATGAGGAAGTGAACCGGTGGTGGACGTGCTGGAGAGATCCCTGTTTCGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAGCCGgtaacttttcaatatacacttaatggatgttgatgtttcattgtactcctctcttaaaacgacatctgggactgggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT