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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttgacgctgacttgttagtttttgttgtttgttttgctcccagggtattgaaatatatgtttcactcctttattcttgcccacatcgcag

Basic information

species Oryza sativa
transcript LOC_Os03g50480.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 6
CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttgacgctgacttgttagtttttgttgtttgttttgctcccagggtattgaaatatatgttt-cactc-ctttattcttgcccacatcgcag
 |||| |||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| |||||| | |||||||||||||||||| || |    ||  || ||  |  | || || | |||||   |  |||| || || |||||   ||| | ||| ||||| |  |||           
TATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattcagtgccaacctgccaagtatt-ttctctgtttctttgacaggttagtggaatattcattttctctcactttactactgcag---------

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 6
CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttgacgctgacttgttagtt-tttgttgtttgttt-tgctcccagggtattgaaatatatgtttcactcctttattcttgcccacatcgcag
||||| ||||||||| ||||| |||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| |||||| | |||||||| ||||||||| || |  | |   || || ||  | |||  |    |||| |  |  |||| || || | ||| | |||  |||||   ||  |||   ||      
CATGGGAAATGGTGGGCCTGCTCCTGAATCTGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTACCAGATgtatgattcaatgtcaacctgctaactatttactcaccgtttattttaacaggttagtggattatttatttt-ctcctactttactgct-gcag-----
















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|58695799|gb|CK084486.1|CK084486
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58693865|gb|CK082552.1|CK082552
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58654844|gb|CK043524.1|CK043524
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|15008682|gb|AU223070.1|AU223070
EST:     TCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: TCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58666397|gb|CK055083.1|CK055083
EST:     TAATACAACGACAATTACTGAATATCTCATCGGCGGAAGACCTTCCAGAT                         GTCGATATTTC
genomic: TAATACAACGACAATTACTGAATATCTCATCG-CGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTC
EST: gi|58602722|gb|CK013250.1|CK013250
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
EST: gi|58667790|gb|CK056476.1|CK056476
EST:     CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGAT                         GTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT
genomic: CTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCT

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: 75 (upstream exon), 71 (downstream exon)
Score: 128

CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttg ... cacatcgcagGTCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCTTTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttgacgctgacttgttagtttttgttgtttgttttgctcccagggtattgaaatatatgtttcactcctttattcttgcccacatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA