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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttag

Basic information

species Oryza sativa
transcript LOC_Os04g59040.1
intron # 7
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 7
ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctca---tagtccgttttatggtttaa-attgcatatcccata-------tagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttag
||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||| || |||||||||||||| |||||||||    || | | |||  || |||   | | || || |  ||       | | ||  |     ||| |||   |    |     |||||| | ||||  | | ||
ATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGATCAAGCGCTTCTTTGAAGATTgtatcctccgcttaattcatttgctgttttcttactacacatgctctagcatattttggatgatcacattcacgcaggtaggcatatgcttccttagcgatat-ctctcag

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G061928_T02 (Zea mays), 5'ss of exon 7
ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcatagtccgttttatggttta--aattgcatatcccatatagtatagt---attggtcatgcatacatctgttattgtccttaacaatatgtttttag
|||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||||||||| ||||||||  | |     | ||| ||||    | | || |   | | ||||||| |      | |||     |||  | | |   |||||| |  |||  || |||
ATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGATCAAGCGGTTCTTTGAAGATTgtatcctgctcgattcatctattgttttctgactacacaatgc-tctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtat-cttctag
















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|58669944|gb|CK058630.1|CK058630
EST:     GTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTGGCCTGCCA
genomic: GTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86417243|gb|CI031452.1|CI031452
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88266037|gb|CI376939.1|CI376939
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86498205|gb|CI140838.1|CI140838
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88217144|gb|CI216993.1|CI216993
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|33681023|gb|CF309262.1|CF309262
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGA
EST: gi|88320691|gb|CI525633.1|CI525633
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88985582|gb|CI016291.1|CI016291
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86523613|gb|CI163819.1|CI163819
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|89171018|gb|CI040295.1|CI040295
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86873424|gb|CI341649.1|CI341649
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|33681024|gb|CF309263.1|CF309263
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88384252|gb|CI551178.1|CI551178
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|58603027|gb|CK013555.1|CK013555
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|11026234|gb|AU162835.1|AU162835
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|163918341|gb|EG713193.1|EG713193
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|218494174|gb|FG955165.1|FG955165
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|55434347|gb|CV730295.1|CV730295
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|87007333|gb|CI279004.1|CI279004
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|58671895|gb|CK060581.1|CK060581
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATG
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATG
EST: gi|8527453|gb|AU092268.1|AU092268
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88450730|gb|CI549816.1|CI549816
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86834579|gb|CI340696.1|CI340696
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88291938|gb|CI532530.1|CI532530
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88963306|gb|CI028322.1|CI028322
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88441295|gb|CI538738.1|CI538738
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|3768325|gb|AU032352.1|AU032352
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88555507|gb|CI485770.1|CI485770
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGAGT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86527296|gb|CI167502.1|CI167502
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88965200|gb|CI009236.1|CI009236
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88984409|gb|CI014964.1|CI014964
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86846050|gb|CI347237.1|CI347237
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86421029|gb|CI057018.1|CI057018
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA

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 1 RNA-Seqlibrary.


Block sizes: 29 (upstream exon), 66 (downstream exon)
Score: 53

ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA