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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggatatttttctagtaacttataacatatattaagcatatgtttattcactgatgtcaccttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG

Basic information

species Zea mays
transcript GRMZM2G074037_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g40560.1 (Oryza sativa), 3'ss of exon 5
gtctggatattttt-----ctagtaact-tataacatatattaagcatatgtttattcactgatgt-caccttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG
|||||  | |||||      ||| |||  | | | | ||  ||   |||||||||   ||||||||  || ||| |||||| | |||||||||||||||||||| || ||||| ||||||||||||||  | ||  | || ||||||  ||||||||| |||||||| 
gtctgtttttttttaatgtttagcaaccatttcagacatgctagatatatgttta---actgatgtgtacttttaaaacagATTGTGTCAAGTGCTATCATTGACAAGTACATAGGTGAAAGTGCACGTCTCATAAGAGAGATGTTTTCCTATGCACGGGAGCATCAA

upper sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G01200.1 (Glycine max), 3'ss of exon 7
----------------------gtctggatatttttctagtaacttataacatatattaagcatatgtttattcactgatgtcaccttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG
                      || || | |   | || |     | | | |   | |||  | ||   ||   |    | |    || |   ||||| || || ||| |||| ||| ||||||  ||||||||||||||| | |||||| | ||||||||||| ||||| ||  | ||||||
gttcaactcttgtctttgtgctgtgtgaacaaagtgcttgatgggtgttataataaataaataaataaataaa-atatttttttttttcttttcagGTTGTATCTAGTACTATAATTCATAAATCTATTGGTGAAAGTGCAAGATTAATTAGGGAAATGTTTAAATATGCCCGCAATCATCAG

upper sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ13668 (Selaginella moellendorffii), 3'ss of exon 5
gtctggatatttttctagtaacttataacatatattaagcatatgtttattcactgatgtcaccttt-taaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG
                 |||| || | | |    | |||    | |||     || | |    ||   |  |||||||||||| ||||||||| | || || ||||||||||| ||||| ||  |||| |||||||||||   |||||| ||||| || || 
-----------------gtaagttttgaaaagcttgaagt---tctttgcgtgctaaggctgtctacgtttacagGTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA

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|211391774|gb|FL355250.1|FL355250
EST:     CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAG                         GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTS-ACGCTTA
genomic: CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTA
EST: gi|211044167|gb|FL460078.1|FL460078
EST:     CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAG                         GTGGTGTCAAGTGCTATCATTGATAAATACATT
genomic: CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATT
EST: gi|211075772|gb|FL462562.1|FL462562
EST:     CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAG                         GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTA
genomic: CGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTA
EST: gi|211416916|gb|FL328808.1|FL328808
EST:     AGCAACATTGATGCTAATTTTTTGAAG                         GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTA
genomic: AGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTA

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: 47 (upstream exon), 47 (downstream exon)
Score: 108

GGCGTGCTGCTCTACGGTCCACCTGGAACTGGGAAGACGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 72

GGCGTGCTGCTCTACGGTCCACCTGGAACTGGGAAGACGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 88

GGCGTGCTGCTCTACGGTCCACCTGGAACTGGGAAGACGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 118

GGCGTGCTGCTCTACGGTCCACCTGGAACTGGGAAGACGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAGgtctggatat ... ttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttataacatatattaagcatatgtttattcactgatgtcaccttttaaacagGTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG
                                        tcacctttt  CT-rich tract
     ataacatatattaagc  TA-rich tract