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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgtcaaacaataaggcattttcttttgtcgttaccctgtaggagtttattaatctcagtgcgtgcttctttccctcccacag

Basic information

species Zea mays
transcript GRMZM2G010596_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010596_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g12560.1 (Oryza sativa), 5'ss of exon 4
GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtg----------------tgtcaa--acaataaggcattttcttttgtcgttaccctgtaggagtttattaatctcagtgcgtgcttctttccctcccacag
||||| || ||||||||||||||||||||| ||||||| ||||| |||||||||| || ||                | ||||   || ||||    |||  ||||  || |        ||| | |  ||| |   |    ||||  | | || |  |||
GTCTTAGTTTACCATGACTTGTTAGGGATGATGCAACATCCACACCATGCCAAGgtaaatgacacttgacaccatcctttcaatgtcagtaagcagctttgctttgatgtgagttgtgccgagctgaacaatttgtataatcgcttactgctctactgcag
















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|149096806|gb|EE182592.2|EE182592
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCCAG                         GTCACACCAAAATTCTGTA
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTA
EST: gi|87155899|gb|DY400688.1|DY400688
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTAATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|149100426|gb|EE186501.2|EE186501
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|76014403|gb|DT941573.1|DT941573
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|149112325|gb|EE295216.2|EE295216
EST:     TGGTGTACCATGACTTGTTAGGGATGGTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGGGATGTCATCACC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|78074144|gb|DV502578.1|DV502578
EST:     GACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: GACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|148963379|gb|EE014384.2|EE014384
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACA
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACA
EST: gi|50326184|gb|CO521310.1|CO521310
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|71762021|gb|DR959958.1|DR959958
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|74234159|gb|DT642073.1|DT642073
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|89247322|gb|DY619108.1|DY619108
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|76925026|gb|DV170254.1|DV170254
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|148949338|gb|EC894792.2|EC894792
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGGGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|91869927|gb|EB400612.1|EB400612
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|78074143|gb|DV502577.1|DV502577
EST:     GACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: GACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|50331354|gb|CO526480.1|CO526480
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|71311050|gb|DR791837.1|DR791837
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCNAG                         GTCACACCAAAATTCTGT
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGT
EST: gi|50326633|gb|CO521759.1|CO521759
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|50330324|gb|CO525450.1|CO525450
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|78114102|gb|DV532491.1|DV532491
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|211281935|gb|FL354664.1|FL354664
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGT
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGT
EST: gi|148986221|gb|EE029969.2|EE029969
EST:     TGGTGTACCATGACTTGTTAGGGATGGTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTTTGTAAACAATTTGGTAACGTGGGGGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|32932859|gb|CF037671.1|CF037671
EST:     GGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: GGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|89252520|gb|DY624306.1|DY624306
EST:     GGGTGTACCATGACTTTTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGGGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|71766836|gb|DR964773.1|DR964773
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|91049382|gb|EB159800.1|EB159800
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC
EST: gi|148981404|gb|EE027628.2|EE027628
EST:     TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAG                         GTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGGGATGTCATCAAC
genomic: TGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAAC

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: 46 (upstream exon), 36 (downstream exon)
Score: 8

GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAACAAGGCGCTATCAGAGTACAAGCAAGAAGTGGAGGCTCAGGCTTTCCCTG


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 18

GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAACAAGGCGCTATCAGAGTACAAGCAAGAAGTGGAGGCTCAGGCTTTCCCTG


Block sizes: 37 (upstream exon), 45 (downstream exon)
Score: 5

GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAACAAGGCGCTATCAGAGTACAAGCAAGAAGTGGAGGCTCAGGCTTTCCCTG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 47

GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgt ... cctcccacagGTCACACCAAAATTCTGTAAACAATTTGGTAACGTGGGCGATGTCATCAACAAGGCGCTATCAGAGTACAAGCAAGAAGTGGAGGCTCAGGCTTTCCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTGGTGTACCATGACTTGTTAGGGATGCTGCAACACCCACATCATGCCAAGgcaagtgtgtcaaacaataaggcattttcttttgtcgttaccctgtaggagtttattaatctcagtgcgtgcttctttccctcccacag

- - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - TGCTGC