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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagttagtagtactttgctcttctcagtttgatatgtgcttgctattcctatacttctctcactttcatctactcttcaacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAATTTTGATCCTAGTTCTTATGATGGAGATGTTCTACCTGAAACCGACAAT

Basic information

species Oryza sativa
transcript LOC_Os07g13170.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g13170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G176175_T01 (Zea mays), 3'ss of exon 6
gttcagttagtagtactttgctcttctc---agtttgatatgtgct------tgctatt--cctatact-tctctcactttcatctactcttcaact-tgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAATTTTGATCCTAGTTCTTATGATGGAGATGTTCTACCTGAAACCGACAAT-
|||||||||| |||| | ||| |||||    | |||    | |  |      |||||    | || ||| || | |||||| ||||  |  |  | | |||||||| |||||  ||||||| || ||||||||||||  ||| |||||||  || |||||| ||  ||| |||||||||||||| | || |  | ||  |||| 
gttcagttagcagtattgtgcacttcttttaaatttttcgtatattcatggatgctaacaacttaaactctcacgcactttgatctctttgttgattctgtagAGCGTATGATAGGGCAGCCATTCGCTTCAATGGACCGGATGCTGTTAGGAACTTTGATTCTGTTTCCTATGATGGAGATGTCCCACTTCCA-CCTGCAATT
















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|88741773|gb|CI765281.1|CI765281
EST:     GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAG                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
genomic: GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAGgttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
EST: gi|29677592|gb|CB673867.1|CB673867
EST:     CA                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
genomic: --gttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
EST: gi|29677592|gb|CB673867.1|CB673867
EST:     CA                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
genomic: --gttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
EST: gi|29677592|gb|CB673867.1|CB673867
EST:     CA                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
genomic: --gttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
EST: gi|29677592|gb|CB673867.1|CB673867
EST:     CA                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
genomic: --gttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
EST: gi|29677592|gb|CB673867.1|CB673867
EST:     CA                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
genomic: --gttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTA
EST: gi|58673756|gb|CK062442.1|CK062442
EST:     GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAG                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
genomic: GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAGgttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
EST: gi|157651263|gb|EX450897.1|EX450897
EST:     GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAG                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
genomic: GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAGgttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
EST: gi|58587235|gb|CF985543.1|CF985543
EST:     GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAG                         AGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA
genomic: GTACATCTATCTAGGATTGTTTGACAGTGAAATTGAGGCTGCAAGgttcagttag ... caacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgcttgctattcctatacttctctcactttcatctactcttcaacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAATTTTGATCCTAGTTCTTATGATGGAGATGTTCTACCTGAAACCGACAAT
                        ctctcac  putative branch site (score: 3)
                   tacttctctcactttc  CT-rich tract
                 tatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagttagtagtactttgctcttctcagtttgatatgtgcttgctattcctatacttctctcactttcatctactcttcaacttgtagAGCATATGACCGGGCAGCTATCCGCTTCAATGGAAGGGAAGCTGTTACTAATTTTGATCCTAGTTCTTATGATGGAGATGTTCTACCTGAAACCGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG