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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtattatattacatggaactctggcatgaaaagaatagaaagaggattgcttaaattctcctgatgtcaaatgatcatgttaattacagcacagcccaatgcagctattgttttaggaggaatactattttaattcattaacaactctaagatgtctaatgcacgttttcttctcttgacag

Basic information

species Zea mays
transcript GRMZM5G885392_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 4
GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtattatattacatggaactctgg---catgaaaagaatagaaagaggattgcttaaattctcctgatgtcaaatgatc-atgttaatta--cagcacagcccaatgcagctattgttttaggaggaatactattttaattcattaacaactctaag-atgtctaatgcacgttttcttctcttgacag
|||||||||||||||||||| || ||||| |||||||| || ||||||||||| ||||| ||| |||||||| ||||||||| || |||| |||||        |   |||        |  |    |   || ||||  | |  |    | |   |||  ||| | |||   ||   |     |       ||||||||| ||  |  |  | |||   |  | |||  ||| |    || ||||||  |  |||  |  ||       
GTCTACAGTGACTTGACTGTCGATTACTTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcag--ttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtcttcacag---
















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|18178811|gb|BM380021.1|BM380021
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|32924858|gb|CF029670.1|CF029670
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTCTTGGATGATTTCACGAGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|71760700|gb|DR958637.1|DR958637
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|32925008|gb|CF029820.1|CF029820
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|32926006|gb|CF030818.1|CF030818
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|6827379|gb|AW331022.1|AW331022
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGCTGTAGCTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGNATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|32926318|gb|CF031130.1|CF031130
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|78074964|gb|DV503398.1|DV503398
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|13381842|gb|BG458517.1|BG458517
EST:     TATATTATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: -A-A-GATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|148942558|gb|EC887577.2|EC887577
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGTTCTGGCACT                         ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATTTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|32942294|gb|CF047113.1|CF047113
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACT                         ATTCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA
EST: gi|110538710|gb|EE042664.1|EE042664
EST:     TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTTTGGCACT                         ATTTTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATTTTCTTGA
genomic: TTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGA

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), 26 (downstream exon)
Score: 8

GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 90

GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 1

GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 96

GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtatta ... ctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTACAGTGACTTGACTGTTGACTACTTGAAGATGTTGCTCCTAAATGTTCCCGCAGCTGTTGTAGCTCTGGCACTgtgagtattatattacatggaactctggcatgaaaagaatagaaagaggattgcttaaattctcctgatgtcaaatgatcatgttaattacagcacagcccaatgcagctattgttttaggaggaatactattttaattcattaacaactctaagatgtctaatgcacgttttcttctcttgacag

- - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT