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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcttactctgctgggagttgttgacagatcctgtataactgcatgacaatagtaacatgtcaaacctttgcgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG

Basic information

species Zea mays
transcript GRMZM2G155836_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 5
gtaaagcttactctgctgggagttgttgacagatcctgtataactgcatgacaatagtaacatgtcaaacct-ttgcgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG
|||| | |||| |  || |   || |   |    |  | | || |        |   |||||||  |||||| ||   ||| |||||| || ||||| ||||| ||||||||||||| |||||| ||||| |||||||| || ||||| |||||||| |||
gtaacg-ttacacacctagatcttctaatctatcctagcacaattatgcattgagtataacatggaaaacctattataattgacagATATGCAGAGCTTTGGCGTACATTCACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG
















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|71315008|gb|DR794124.1|DR794124
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|87154289|gb|DY399078.1|DY399078
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|149111565|gb|EE190699.2|EE190699
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGA
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGA
EST: gi|89253101|gb|DY624887.1|DY624887
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCA
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCA
EST: gi|76927490|gb|DV171263.1|DV171263
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|21390766|gb|BQ528815.1|BQ528815
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGNATATGTATCAG                         ATTTGGAGAGCCTTGGCATACATTCACAACAGCATTG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTG
EST: gi|148971909|gb|EE022686.2|EE022686
EST:     AGATGACCCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCCCAACAGC
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGC
EST: gi|211069077|gb|FL187242.1|FL187242
EST:     ATGCAAAACTGTATATGTATCAG                         ATCTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: ATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|149009140|gb|EE041278.2|EE041278
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCCCAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|149078458|gb|EE167238.2|EE167238
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATT
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATT
EST: gi|6626369|gb|AW257901.1|AW257901
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|148961324|gb|EE012052.2|EE012052
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|74234442|gb|DT642356.1|DT642356
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|149095924|gb|EE181586.2|EE181586
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
EST: gi|71446043|gb|DR827093.1|DR827093
EST:     AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAG                         ATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG
genomic: AGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGG

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: 96

GCTTGAGTATGTACCGGAGACTGCTCATCGTGTCATCAAACATTACAACAAGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GCTTGAGTATGTACCGGAGACTGCTCATCGTGTCATCAAACATTACAACAAGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GCTTGAGTATGTACCGGAGACTGCTCATCGTGTCATCAAACATTACAACAAGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GCTTGAGTATGTACCGGAGACTGCTCATCGTGTCATCAAACATTACAACAAGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgtaaagctta ... cgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcctgtataactgcatgacaatagtaacatgtcaaacctttgcgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG
                        tagtaac  putative branch site (score: 133)
                                       cctttgc  putative PPT
                      aatagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcttactctgctgggagttgttgacagatcctgtataactgcatgacaatagtaacatgtcaaacctttgcgattcacagATTTGTAGAGCCTTGGCATACATTCACAACAGCATTGGAGTGTGCCACAGGGACATTAAGCCGCAAAATCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG