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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
----atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA
     | | ||| ||||   |      | || |  |  | |||||| ||| ||||     | |   ||||| | |||| | |    ||||||| | | || ||| | | ||||||||| || |||||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||
gtctctgtagctctaagctgtt----cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
















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|89253086|gb|DY624872.1|DY624872
EST:     CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|60338155|gb|DN205128.1|DN205128
EST:     CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|78122763|gb|DV541147.1|DV541147
EST:     ACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: ACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|78122764|gb|DV541148.1|DV541148
EST:     CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|60340849|gb|DN207822.1|DN207822
EST:     CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|211449937|gb|FL278245.1|FL278245
EST:     TGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: TGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
EST: gi|71435773|gb|DR816823.1|DR816823
EST:     CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGAT                         GCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT
genomic: CAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCT

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: 417

GGTGATGTTTATCCTGTGGAATCTTACGAGAGCTTATCAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GGTGATGTTTATCCTGTGGAATCTTACGAGAGCTTATCAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

GGTGATGTTTATCCTGTGGAATCTTACGAGAGCTTATCAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 203

GGTGATGTTTATCCTGTGGAATCTTACGAGAGCTTATCAGTGAACCATGTACTTGATGCTCATTGGGGTGTTCTGGATGATGATGATgtaagtatag ... tgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA
                                  tattgatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

- - - - - aagaaatg
- - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcta