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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttttccaaatcggtagttatgtaatggcatggatccaattaatcctaatgataatgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG

Basic information

species Oryza sativa
transcript LOC_Os07g17400.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171967_T01 (Zea mays), 3'ss of exon 1
--tacttttccaaatcggtagttatgtaatggcatggatccaattaatcctaatgataatgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
  ||| |   ||        ||  |||    |  |   | |   |      | || |  | |||||| |  | |  | |||   ||  ||  |||||| ||||||  ||||||| |||||||| |||||||| |||||||||||||||||| |||||| |||||| ||||| ||||| ||| | ||| ||||||| ||||||
aatacatgggcatccaaaaggtcttgtgtgtgtttcattgctgctgtggtgattggt--taggttggaccgtttcaacttacttctgattcgcaaattccagGGCAGATGCTATTCAGAGGAATTATGGTGGCGCATGTGTGCAGATGAGGCTGTCGTTCAGCTCCCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTG

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G342711_T01 (Zea mays), 3'ss of exon 1
tacttttccaaatcggtagttatgtaatggcatgg--atccaattaatcctaatgataatgggttggtcgt-tgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
   |        | || | | | || |   |||||  ||||||    || |    ||  |    || |  | || |||||  | |  | |   | |||| ||||||  ||||||| |||||||| ||||||||| ||||||||||||||||| |||||| |||||| || || ||||| ||  | ||| ||||||| ||| ||
-tgtggattgtgttgg-attaaggtgaatacatgggcatccaaaaggtcttgtgtatgtttcactgctgctgtgatgattggttaggt-tggaccaattccagGGCAGATGCTATTCAGAGGAATTATGGTGGATCATGTGTGCAGATGAGGCTGTCGTTCAGCTCTCTAGCTCCATTGTTCTTGTACTTCATCCAATGGTTG

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G439168_T02 (Zea mays), 3'ss of exon 2
tacttttccaaatcggtagttatgtaatg-gcatggatccaattaatcctaatgataa--tgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
    |  | ||    | |   | ||  || | |||  ||          | |||||    | |||||| |  | |  | |||   ||  ||  |||||| ||||||  ||||||| |||||||| ||||||||| ||||||||||||||||| ||||||  ||||| ||||| ||||| ||  | ||| | ||||| ||||||
---ctaacaaagggagcaagaaggtcttgtgtatgtttcactgctgctgtgatgattggttaggttggaccatttcaacttacttctgattcacaaattccagGGCAGATGCTATTCAGAGGAATTATGGTGGATCATGTGTGCAGATGAGGCTGTCGTTTAGCTCTCTGGCTCCATTGTTCTTGTACTTTATCCAATGGCTG

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067329_T01 (Zea mays), 3'ss of exon 1
tacttttccaaatcggtagttatgtaatggcatgg--atccaattaatcctaatgataatgggttggtcgt-tgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
   |        | || | | | || |   |||||  ||||||     | |    ||  |    || |  | || |||||  | |  | |   | |||| ||||||  ||| ||| |||||||| ||||||||| ||||||||||||||||| |||||| |||||| ||||| ||||| ||  | ||| ||||||| ||||||
-tgtggattgtgttgg-attaaggtgaatacatgggcatccaaaagggcttgtgtatgtttcactgctgctgtgatgattggttaggt-tggaccaattccagGGCAGATGTTATTCAGAGGAATTATGGTGGATCATGTGTGCAGATGAGGCTGTCGTTCAGCTCTCTGGCTCCATTGTTCTTGTACTTCATCCAATGGCTG

upper sequence: LOC_Os07g17400.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G011562_T01 (Zea mays), 3'ss of exon 1
--tacttttccaaatcggtagttatgtaatggcatggatccaattaatcctaatgat--aatgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
  ||| |   ||        ||  |||    | |||  ||          |  ||||   || |||||| |  | |  | |||   ||  ||  || ||| ||||||  ||||||| |||||||| ||||||||  ||||||||||||||||| |||||| |||||| || || ||||| ||| | ||| ||||||| ||||||
aatacatgggcatccaaaaggtcttgt----gtatgtttcactgctgctgtggtgattggataggttggaccgtttcaacttacttctgattcacatattccagGGCAGATGCTATTCAGAGGAATTATGGTGGGTCATGTGTGCAGATGAGGCTGTCGTTCAGCTCCCTAGCTCCATTGTTTTTGTACTTCATCCAATGGCTG

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|33684776|gb|CF313015.1|CF313015
EST:     AGAGGGCCCCTCAAGGCACTGGAGGCCGACATCCACCATGCCAACACCAT                         GGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTT
genomic: AGAGGGCCCCTCAAGGCACTGGAGGCCGACATCCACCATGCCAACACCATgtgagcgctc ... caaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTT
EST: gi|33685850|gb|CF314089.1|CF314089
EST:     AGAGGGCCCCTCAAGGCACTGGAGGCCGACATCCACCATGCCAACACCAT                         GGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTT
genomic: AGAGGGCCCCTCAAGGCACTGGAGGCCGACATCCACCATGCCAACACCATgtgagcgctc ... caaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctaatgataatgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG
                        tgttgat  putative branch site (score: 4)
                                     cttgtttcc  putative PPT
                          ttgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttttccaaatcggtagttatgtaatggcatggatccaattaatcctaatgataatgggttggtcgttgttgatttatgacttgtttccaaatttcagGGCTAATGCTATCCAGAGGAACTATGGTGGAGCATGTGTGCAGATGAGGTTGTCGTGCAGCTCACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA