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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttaacctttaaattgctggcacttagctttaccccaccattttgcattaccctgtttgctttttttaaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
-----gttagtttaacctttaaattgctggcacttagctttaccccacca-ttttgcattaccctgtttgctttttttaaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG
      ||  |  |||||| |||||| | ||| || |    |   ||    || |||  |   ||       |  | | || | |||  |||  |||||||||||||| ||| ||||||| || |||||||| || ||||| || || |||||||| || |||||||| ||
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgctctttgct-cagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
















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|33099519|gb|CF059479.1|CF059479
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGT
EST: gi|31349785|gb|CD434142.1|CD434142
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
EST: gi|71426924|gb|DR807974.1|DR807974
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
EST: gi|74245361|gb|DT653275.1|DT653275
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
EST: gi|74232804|gb|DT640718.1|DT640718
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCAT
EST: gi|211310239|gb|FL338849.1|FL338849
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCAATGTGGGGTACCGCACAGCTCTTTATGGCA
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATG-CA
EST: gi|32844196|gb|CD983877.1|CD983877
EST:     AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAG                         GGTGAGACCAATATAAAGCCATTGTGGGGT
genomic: AAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGT

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: 245

GAAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

GAAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341

GAAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GAAACAAATTCTAACTTGGATGAGATAGTCCAGCTGGCAAAGCAGCTGCAGgttagtttaa ... ttccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttaccccaccattttgcattaccctgtttgctttttttaaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG
                                             ttccattt  CT-rich tract
                                   tttttttaaattccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttaacctttaaattgctggcacttagctttaccccaccattttgcattaccctgtttgctttttttaaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT