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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatgcaaaatccagaggatgcacaggataattatcatgtccatgctgaatctctatgctatatgaaactttagattcattcttcacttgactactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAACTTCCTTGTGGGCACCATTTCCACTGTGCCTGCATTGATAAATGGCTGC

Basic information

species Oryza sativa
transcript LOC_Os04g48050.1
intron # 4
splice site 3'
intron type U2

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|58682495|gb|CK071182.1|CK071182
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|29641515|gb|CB646522.1|CB646522
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|38479871|gb|CF963960.1|CF963960
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|27577289|gb|CA999983.1|CA999983
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|15850493|gb|BI798769.1|BI798769
EST:     AGTGTGGCACC-ATCAACCTATTGAGAAAGTACTCGCACCTGAAGAT-CG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|88272113|gb|CI388166.1|CI388166
EST:     AGT-TGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|58685141|gb|CK073828.1|CK073828
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|29669615|gb|CB665890.1|CB665890
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|86849654|gb|CI299790.1|CI299790
EST:     TGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: TGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|29669617|gb|CB665892.1|CB665892
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|29663345|gb|CB659620.1|CB659620
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|58683789|gb|CK072476.1|CK072476
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|218487087|gb|FG954413.1|FG954413
EST:     AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
EST: gi|25803791|gb|CA759752.1|CA759752
EST:     AGTGTGGCACCAATCAACCTACTGAGAAAGTACTCGCACCTGAAGATGCG                         GAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA
genomic: AGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAA

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: 61 (upstream exon), 69 (downstream exon)
Score: 30

TGAAAAACAAACTGCTGATGAGACAGGACCTTTTGGTGGAATAATGACAGAGTGTGGCACCAATCAACCTATTGAGAAAGTACTCGCACCTGAAGATGCGgtaagttttt ... actactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAACTTCCTTGTGGGCACCATTTCCACTGTGCCTGCATTGATAAATGGCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaatctctatgctatatgaaactttagattcattcttcacttgactactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAACTTCCTTGTGGGCACCATTTCCACTGTGCCTGCATTGATAAATGGCTGC
                                        acttgac  putative branch site (score: 30)
              tatatgaaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatgcaaaatccagaggatgcacaggataattatcatgtccatgctgaatctctatgctatatgaaactttagattcattcttcacttgactactgcagGAGTGTTGCATTTGCCTTTCGGCATATGATGATGGTGCAGAGCTGCGTGAACTTCCTTGTGGGCACCATTTCCACTGTGCCTGCATTGATAAATGGCTGC

ctatgca
- - - - - - - - ggatgca
- - - - - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tctatgc