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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataaccgcaacccatcgtctagatggctattatgaagtttactatgttgtttgtaacatctcattttgtttcacttcag

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataac----cgcaacccatcgtctagatggctattatgaagtttactatgttgtttgtaac--atctcattttgtttcacttcag---------------------------
||||||| ||||||| ||||||||| ||||||| ||||||||||||||||| ||||| ||||||||||||||    ||||||||| | || |||||||||||| | |      | |      || || | ||   ||||||  | |  | |  |   | |  ||    ||   | || |    || |                             
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattattta-tcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
















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|148974317|gb|EE025090.2|EE025090
EST:     AGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTGGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: AGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211061849|gb|FL232858.1|FL232858
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|113701122|gb|EE678626.1|EE678626
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|37374425|gb|CF623569.1|CF623569
EST:     GAATGGTTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTCGATAGCTCCAAAACCCAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|60353207|gb|DN220180.1|DN220180
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|60398924|gb|DN231740.1|DN231740
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|60340539|gb|DN207512.1|DN207512
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|60344210|gb|DN211183.1|DN211183
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211061848|gb|FL232857.1|FL232857
EST:     CGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: CGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211021947|gb|FL480535.1|FL480535
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|60398791|gb|DN231607.1|DN231607
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|74239509|gb|DT647423.1|DT647423
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211061847|gb|FL232856.1|FL232856
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|61119293|gb|DN560254.1|DN560254
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGC
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGC
EST: gi|60399770|gb|DN232580.1|DN232580
EST:     GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: GAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211061850|gb|FL232859.1|FL232859
EST:     CGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: CGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
EST: gi|211061851|gb|FL232860.1|FL232860
EST:     TAGTCCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG
genomic: TAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATG

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: 210

GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATGGAAGGCAGGTACCTCCGTGATGTATGGTGACACATCACCCCCATTCAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 268

GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATGGAAGGCAGGTACCTCCGTGATGTATGGTGACACATCACCCCCATTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATGGAAGGCAGGTACCTCCGTGATGTATGGTGACACATCACCCCCATTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 423

GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataacc ... ttcacttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTACGTAAAGAGCCTGCAGATGGAAGGCAGGTACCTCCGTGATGTATGGTGACACATCACCCCCATTCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataaccgcaacccatcgtctagatggctattatgaagtttactatgttgtttgtaacatctcattttgtttcacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG