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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcttttctgataactttgcatcaatctagtaatcccgtttaaaaatataccaatcccacactaaattttctgtcttttcatgttattatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAATGAAGCCATGTATGGGCAGTTGCTCTCTAAATATCTTGACGATCCGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g20270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g20270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G016827_T03 (Zea mays), 3'ss of exon 5
gtactttcttttctgataactttgcatcaatctagtaatcccgtttaaaa-atataccaatcccacactaaattttctgtcttttcatgttattatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAATGAAGCCATGTATGGGCAGTTGCTCTCTAAATATCTTGACGATCCGAAG------------------------------------------
|||  | ||||  | |||    || ||  || ||| | |    ||  ||  | |  | |||| |  |  | ||||| | |||||   ||||   || | | |||||||| || ||||| |||||||||||||||||||| |||| ||||||||| |||||| ||||||||||| ||||||| |||||| | || || || ||                                           
gtaaatcctttgttaata---ctgtattcatttaggagtgtttttggaaccaaactctaatctctaaacacattttatctctttctgtgttg--atttaatagacataatgtgaaagtcgtccctatccttgttggtgcacttagCTCCCAAAACGAAGCCTTGTATGGGCAGCTGCTCTCCAAATATGTGGATGACCCAAAAAACTTCTTTTCCGTGTCGTCAGACTTCTGCCATTGGGGATCC

upper sequence: LOC_Os08g20270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G016827_T02 (Zea mays), 3'ss of exon 5
gtactttcttttctgataactttgcatcaatctagtaatcccgtttaaaa-atataccaatcccacactaaattttctgtcttttcatgttattatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAATGAAGCCATGTATGGGCAGTTGCTCTCTAAATATCTTGACGATCCGAAG
|||  | ||||  | |||    || ||  || ||| | |    ||  ||  | |  | |||| |  |  | ||||| | |||||   ||||   || | | |||||||| || ||||| |||||||||||||||||||| |||| ||||||||| |||||| ||||||||||| ||||||| |||||| | || || || || 
gtaaatcctttgttaata---ctgtattcatttaggagtgtttttggaaccaaactctaatctctaaacacattttatctctttctgtgttg--atttaatagACATAATGTGAAAGTCGTCCCTATCCTTGTTGGTGCACTTAGCTCCCAAAACGAAGCCTTGTATGGGCAGCTGCTCTCCAAATATGTGGATGACCCAAAA
















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|40486364|gb|BX897928.1|BX897928
EST:     GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGG                         ACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAA
genomic: GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGGgtactttctt ... tatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAA
EST: gi|38476889|gb|CF961022.1|CF961022
EST:     GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGG                         ACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAA
genomic: GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGGgtactttctt ... tatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAA
EST: gi|66917040|gb|CX103888.1|CX103888
EST:     GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAA-GTTTTTCAGGG                         ACATAAACG-AAAAGTTGGCCCTATCCTT
genomic: GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGGgtactttctt ... tatcttacagACATAA-CGTAAAAGTTGTCCCTATCCTT
EST: gi|58678103|gb|CK066790.1|CK066790
EST:     GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGG                         ACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTA
genomic: GAACATAGCATGGAAATGCATTTACCCTATCTTTCTAAAGTTTTTCAGGGgtactttctt ... tatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatataccaatcccacactaaattttctgtcttttcatgttattatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAATGAAGCCATGTATGGGCAGTTGCTCTCTAAATATCTTGACGATCCGAAG
                 cactaaa  putative branch site (score: 2)
                                            ttatctt  putative PPT
                                 ttttcatgttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttcttttctgataactttgcatcaatctagtaatcccgtttaaaaatataccaatcccacactaaattttctgtcttttcatgttattatcttacagACATAACGTAAAAGTTGTCCCTATCCTTGTTGGTGCCCTTAACTCCCAAAATGAAGCCATGTATGGGCAGTTGCTCTCTAAATATCTTGACGATCCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC