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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtccttagggcatggtgtcaccccaattattttaaagttatggttgtaataacatcattgttctgatttggttttatgcag

Basic information

species Zea mays
transcript GRMZM2G113592_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113592_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 5'ss of exon 4
GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtccttagggcatggtgtcaccccaattattttaaagttatggttg-taataacatcattgttctgatttggttttatgcag
|| || ||||||| ||| || ||||| | |||||| || ||||| || |||||||| ||||||||||||||||| |||| || |||    | | |   | |  |  ||  | | |  | || | |  | |||||||||||| | || |||   || ||| ||
GCTGAAAAGAAGGATAGGATCCGCAAAAGTAAGCTTGACCAAGGTGCGGCTAAGGTGGCTGAAGAGCTTCAGAAATgtaagttcttt---cttagctgctcttccctttgtatcatatgatagatactgataacatcattggtgtggttt--cttaatgtag
















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|148978947|gb|EE026414.2|EE026414
EST:     AATAAGCTCGAGCAAGGCGCAGCCTAAGGTTGCTGAAGAGCTTCAGAAGT                         ATGACCCACAAAGTGACCCCAATGCTACCTGGAGATCCCTACAAAACACTC
genomic: AATAAGCTCGAGCAAGGCGCAGC-TAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTAC-TGGAGATCCATACAAAACACTC
EST: gi|148967855|gb|EE019150.2|EE019150
EST:     TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGT                         ATGACCCACAAAGTGACCCCAATGC
genomic: TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGC
EST: gi|211227314|gb|FL251475.1|FL251475
EST:     AATAAGCTCGAGCAAGGCGCAGCTTAAG-TTGCTGAAGAGCTTCAGAAGT                         ATGACCCACAAAGTGACCCCCATGGTACTGGAGATCCATACAAAACAC
genomic: AATAAGCTCGAGCAAGGCGCAGCT-AAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACAC
EST: gi|211227311|gb|FL251472.1|FL251472
EST:     TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGT                         ATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCT
genomic: TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCT
EST: gi|91051679|gb|EB162097.1|EB162097
EST:     TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGT                         ATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCT
genomic: TAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCT

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: 136

GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCTTTGTTGCTAGACTT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 107

GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCTTTGTTGCTAGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCTTTGTTGCTAGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtcctt ... ttttatgcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCTTTGTTGCTAGACTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGAAGAAGGCTAGAATTCGCAATAATAAGCTCGAGCAAGGCGCAGCTAAGGTTGCTGAAGAGCTTCAGAAGTgtacgtccttagggcatggtgtcaccccaattattttaaagttatggttgtaataacatcattgttctgatttggttttatgcag

- - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT