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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttttctccttagagatagtttgcaagttgcataatcatgtacactatacgctaatacagtaaagttcaaaattgtctgtctgaagctactatatgcacctacagagtgtcatacctctatatttagtttttatatgttatatcattgtttgaatactcatacttgaagggcag

Basic information

species Zea mays
transcript GRMZM2G168337_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168337_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g50360.1 (Oryza sativa), 5'ss of exon 8
ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttttctccttagagatagtttgcaagttgcataatcatgtacactatacgctaatacagtaaagttcaaaattgtctgtctgaagctactatatgcacctacagagtgtcatacctctatatttagtttttatatgttatatcattgtttgaatactcatacttgaagggcag
||||| ||||||   || ||||||||||  |||||||||| ||| || ||||||||||| ||||| ||||| |||||     ||| |  ||     |   | |  | |||||      | |     |       ||| | | |||||| | | ||| |    | || | |||  |   || || |||| | || | |||    |||| |  | | ||||  | |    |||   | |||||  |||||||||||
ACAACAAAAGCTGGGACGCATGATTCAGAGTCCTGCCTCAGAGAGCAGTCATGCTTGCCTTTAGGAGGACAGAGgtgaccactttttttttct---tgcataggcatttgcacctctgttttggaaagttatggatatatttaagttccacaatgtgttgtggtagttgctacct-tgccaactgagtattat-cgtcttctgttagctagtttttgtttcaac----ttttggttctcatgtttgaagggcag
















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|31354773|gb|CD439130.1|CD439130
EST:     TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAG                         TGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
genomic: TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
EST: gi|78112707|gb|DV531101.1|DV531101
EST:     TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAG                         TGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
genomic: TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
EST: gi|61119794|gb|DN560755.1|DN560755
EST:     TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAG                         TGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
genomic: TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
EST: gi|76021581|gb|DT948751.1|DT948751
EST:     TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAG                         TGTATGGACTTCATTACCGCCACTTAATAACGGATCTAC
genomic: TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTAC
EST: gi|148963596|gb|EE014634.2|EE014634
EST:     TCAGCATCCTGCCTCAAAGACCAATCATGCTTGCCCTTAGGTGGACACAG                         TGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA
genomic: TCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAAACCTTTAATATTGGCTATTGCGTCTCAAGACTCTGCATCATTTTTTCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAAACCTTTAATATTGGCTATTGCGTCTCAAGACTCTGCATCATTTTTTCGG


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

ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAAACCTTTAATATTGGCTATTGCGTCTCAAGACTCTGCATCATTTTTTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttt ... tgaagggcagTGTATGGACTTCATTACCGCCACTTAATAACGGATCTACAGAGCATCCGAAACCTTTAATATTGGCTATTGCGTCTCAAGACTCTGCATCATTTTTTCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAACCAAAGCTCAAACACATGATTCAGCATCCTGCCTCAAAGAACAATCATGCTTGCCCTTAGGTGGACACAGgtgtgttttttctccttagagatagtttgcaagttgcataatcatgtacactatacgctaatacagtaaagttcaaaattgtctgtctgaagctactatatgcacctacagagtgtcatacctctatatttagtttttatatgttatatcattgtttgaatactcatacttgaagggcag

- - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA