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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatcttctgtttggttgatcatgctgttaatgtttggttgtggttgtcatgtaatatgccatgcaaatacctgcaattgtcacttttgttagaac...

Basic information

species Zea mays
transcript GRMZM5G856084_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g26914.2 (Oryza sativa), 5'ss of exon 4
GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatc-ttctgtttggttgatcatgctgt-taatgtttggttgtggttgtcatgtaatatgccatgcaaatacctgcaattgtcacttttgttagaac-
|||||||||     ||||||||| |||||||||||||||||||||||||||||||| ||| ||| |  || | ||||   | | | |   |  | || |||||  |   |   ||   |   |   | |  |    |||   |    || | ||| || | 
GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTGgtaggtgtggttttatttgtcagtttagggcatgcagtgattggtgctccgtacaatcgtaggagtattacccagctttgc---ttcttctctagtttgagcc

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G14290.1 (Glycine max), 5'ss of exon 4
GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatcttctgtttggttgatcatgctgtta-atgtt--tggttgtggttgtcatgtaatatgccatgcaaatacctgca-attgt-cact--tttgttagaac
||||  |||  ||| ||||| || |||||||||||||||||||||||||| |||||    |||||| |||| |||| |   | || ||| || ||| |  |   |    |  | || || |||    || ||||   || | |  ||  | |  |||| ||  | 
GATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAG----TGgtattttctatttgttcccttat-ctgctacatgataatacctccattattaatttattataagttg-aaatgtttgaatacagtgtattgatttgctaata-

upper sequence: GRMZM5G856084_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G31080.1 (Glycine max), 5'ss of exon 4
GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatcttctgtttggttgatcatgctgtta-atgtt--tggttgtggttgtcatgtaatatgccatgcaaatacctg----caattgtcacttttgttagaac
||||  |||  ||| ||||| || |||||||||||||||||||||||||| |||||||||    || |||| |||| |   | || |||||| ||| |  |   |    |  | || || |||    || |||| | ||    || |     | |||| ||  | 
GATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCGgt----attttctatttgttcccttat-ctgttacatgataatacctccattattaatttattataagttg-aaatgcttgaatacagtgtattcatttgctaata-

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|148950667|gb|EC896255.2|EC896255
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
EST: gi|148955679|gb|EC901358.2|EC901358
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
EST: gi|211525859|gb|FL340350.1|FL340350
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
EST: gi|149051735|gb|EE155859.2|EE155859
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
EST: gi|211152737|gb|FL348042.1|FL348042
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
EST: gi|71769003|gb|DR966940.1|DR966940
EST:     TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG                         CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA
genomic: TAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA

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: 43 (upstream exon), 49 (downstream exon)
Score: 133

GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 268

GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 92

GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 197

GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatct ... tattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCGgttggtatcttctgtttggttgatcatgctgttaatgtttggttgtggttgtcatgtaatatgccatgcaaatacctgcaattgtcacttttgttagaac

- - - - - - - - - - - - - AAGAAA