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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatatatttagaagatcaaagatatcgttaataacagataaactgtattgcttctgtgtttattttttgttctgcttttttaatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT

Basic information

species Zea mays
transcript GRMZM2G172322_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172322_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 3'ss of exon 3
gtgagcatatatttagaagatcaaagatatcgttaataacagataaactgtattgctt-ctgtgtttattttttgttctgcttttttaatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT
||||||| |||||  ||| | ||||   ||  || | |  |||| || ||   || |  |||   ||||||||   || |  || |  ||   ||||| ||||||||  |||||||||| |||||| ||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||| || |||
gtgagcaaatattgggaacaacaaaatcat-attcacagtagatgaagtgatctgttcactggagttatttttg--tcgg--ttgtggatttgcagGTCAGAGATTTCATCGCTGAACAGATGTCTCTAAGGGGCATCACATTTCATACTGAACAGAGTCCTCAAGCTATAACCAAATCAAATGATGGTTTGCTAT
















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|32837914|gb|CD977592.1|CD977592
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
EST: gi|18660509|gb|BM500899.1|BM500899
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
EST: gi|134769074|gb|DY742748.1|DY742748
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
EST: gi|211088209|gb|FL308841.1|FL308841
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTYAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
EST: gi|32839140|gb|CD978821.1|CD978821
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
EST: gi|32836456|gb|CD976134.1|CD976134
EST:     TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAG                         GTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT
genomic: TCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCAT

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: 93

GTATATTGCTTTGGAGTTTGCTGGCATTTTCAATGGCTTAAAGAGTGAAGTCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GTATATTGCTTTGGAGTTTGCTGGCATTTTCAATGGCTTAAAGAGTGAAGTCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTATATTGCTTTGGAGTTTGCTGGCATTTTCAATGGCTTAAAGAGTGAAGTCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GTATATTGCTTTGGAGTTTGCTGGCATTTTCAATGGCTTAAAGAGTGAAGTCCATGTGTTTATTCGTCAGAAGAAAGTTTTAAGAGGATTTGATGAAGAGgtgagcatat ... taatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataaactgtattgcttctgtgtttattttttgttctgcttttttaatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT
                                          ttttaat  putative branch site (score: 144)
                       tttattttttgttctg  CT-rich tract
                     tgtttattttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatatatttagaagatcaaagatatcgttaataacagataaactgtattgcttctgtgtttattttttgttctgcttttttaatgcacagGTTAGAGATTTTGTCGCTGAACAAATGTCTTTAAGGGGCATCACGTTTCATACAGAACAGAGCCCTCAAGCTATAACTAAATCAAATGATGGTCTGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT