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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacctttttcccttgcgaccacataatcactagtcaagacccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca...

Basic information

species Oryza sativa
transcript LOC_Os05g51530.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 4
GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtg-------atgacctttttcccttgcgaccacata-----atcactagtcaagacccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca
||| ||||||||||||||||| ||||| || ||||| || ||||||||||| ||||||||||| || ||||||||  ||||||| || ||||||||||||||        | |||     |||  |  |  ||  ||     ||   | |    |||| |  ||    || |  ||||  |||| |  | |  |        |         
GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCCCCTCTCAAGGAGATCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgcacgactccactcctctttgcacatttacgccaatttgttgctgggaccaaggct---catcgctctgtagatatatagcaaaaccggaaacat---------

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 4
GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacctttttcccttgcgaccaca-taatcactagtcaagac--ccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca
||| ||||||||||||||||| ||||| || |||||  ||||||||||||| |||||||||||||| || |||||| ||||||| || ||||||||||||||  |    | |||| | |   || ||  | ||  |  ||||  |    | |   | ||  |      |  | ||     ||   | | |||    |     |
GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAGgt--tcgtttctttctcgtaacacaactctgatgccgggtcagaatgttctataaagattcaccaacatccacat-cacagataatcaggcttgtgcgtacta

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 4
GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgt--gatgacctttttcccttgcgaccacataat--cactagtcaagacccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca-
||| ||||||||||||||||||||||| || ||||| ||||||||||||||||| ||||||||||| ||||||||  |||||||||| ||||| ||||||||  |||  |   | |    |   |  ||| ||   | ||  ||    || | |||   |   || ||||          |  ||| | |  | || || ||   
GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgcacgtcttaagtcttattacacaactccgctcctctctgcctatccttttttgtgtcctgtcccgg----cctgccccagt-ttatcgctggtata

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|29656670|gb|CB652945.1|CB652945
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|29662007|gb|CB658282.1|CB658282
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58595941|gb|CK006469.1|CK006469
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATA
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATA
EST: gi|29612869|gb|CB617882.1|CB617882
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58667113|gb|CK055799.1|CK055799
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58666270|gb|CK054956.1|CK054956
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|218479849|gb|FG959490.1|FG959490
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|218498003|gb|FG943208.1|FG943208
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|33653619|gb|CF276233.1|CF276233
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58686384|gb|CK075071.1|CK075071
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58594698|gb|CF993006.1|CF993006
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGCTCAGGAGCCAGCTTAGTGCGATCAA
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATG-TAAGGAGCCAGCTTAGTGCGATCAA
EST: gi|58600826|gb|CK011354.1|CK011354
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|29613101|gb|CB618114.1|CB618114
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58606956|gb|CK034989.1|CK034989
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58681691|gb|CK070378.1|CK070378
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGG
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGG
EST: gi|58596246|gb|CK006774.1|CK006774
EST:     TGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATTGAAG                         GTTCGAGGAGCGGAATACCATAATGTAAGGAGCCAGCTTAGTGCGATCAA
genomic: TGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACAT-GAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAA
EST: gi|58688997|gb|CK077684.1|CK077684
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|33664188|gb|CF295155.1|CF295155
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|27578007|gb|CB000702.1|CB000702
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|58660817|gb|CK049497.1|CK049497
EST:     TCGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGC
EST: gi|58596714|gb|CK007242.1|CK007242
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|29613962|gb|CB618975.1|CB618975
EST:     TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG                         GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC

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: 73 (upstream exon), 75 (downstream exon)
Score: 64

GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacct ... ttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAGgtgatgacctttttcccttgcgaccacataatcactagtcaagacccaacctacatatagtgctgttaatatgtttcgaccctaatgctgtctctagtca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccaacc