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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgtttacatattgctctgtctaattattcctactctcataatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG

Basic information

species Oryza sativa
transcript LOC_Os07g49270.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 10
gtacttctttctttctttaccaatctcatatttg-------tgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgt--ttacatattgctctg-------tctaattattcctactctca-taatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG
||   |  ||||||| | ||   | |  ||  ||       |  |||||     |  |  | ||     | ||  || | |   ||| |   ||   |||  |||         | || || |  | ||  || |   ||| | ||||||||||||||| | |||||||| |||||||| |||||||| || ||||| || |||||||| ||||||||||| |||||||| || |||||||||||||
gtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG

upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------gtacttctttctttctttaccaatctcat---atttgtgattctttaaggtggtgttgttcgctatttgt-catgtaacacat---tgtttacatattgctctgtctaattattcctactctcataatcttcac---cagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG
                                                  ||||| | || ||    ||||| |        |||    |  |    |      ||| |  |  |      ||  |      |   | |||            ||| | | | ||| |    ||  || |||||   |||||||| ||||||||||| |||||||||||||| ||| ||||||| ||||| ||| | || || ||||| || | |||  || |  | || ||||||||  
gtaaacatctacaacttcttttcaattaaatttttttattagatgtttttgtactccatt-ttgaaataccacttctgcccaattcacaaccccaccacacaaggttttgagtgagcaacacacatgggttttgagtttttgaggggcatgaagtccattgaatcccatcaacagcatattcactttcagATGGCAGAGTATAGAATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGA

upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
gtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacatt-gtttacatattgctctgtctaattattcctactctcataatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG
                 |   || ||| | | | || | ||        ||  | ||     ||     |  ||  | |    || || |      || | |  ||||  |    || |  | |     |||||||||||||||| ||||| || || || || ||||| ||||||||||||||  ||||    ||||| ||  | ||| |  || |||| ||||| ||  
-----------------tgaaaacctcctgtctatgttgct-------agtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacga--tatttgtctgttcgttgtgt-----agATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA

upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 10
gtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaac-acattgtttacatattgctctgtctaattattcctactctcataatcttcac-cagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG
                             ||  | || |      | |    | | |  || ||   | |  ||| ||  ||| | | | || |     | ||| |  |||  |    |     | |   ||||||||||||| || ||||| || || || || ||||| || |||||||||||| ||||||| ||||||||  | |||    ||||||| || || ||  
-----------------------------atacgcgaatggcgttgttaacttggatgacttttaagcgtagaactacggtgtatccgt-ttacaaaaacaaataa--cctgtttatttgtctgtgatgtagATGGCTGAGTACAGGATATCAATTTACGGAAGGAAGAAGAGCGAGTGGGATCAGTTGGCAAGTTGGATAGTTGACAATCGGCTGTACAGTGAAAACGTCA

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|58696016|gb|CK084703.1|CK084703
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|29671780|gb|CB668055.1|CB668055
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|88577196|gb|CI673756.1|CI673756
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|58686177|gb|CK074864.1|CK074864
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|33793650|gb|CF322709.1|CF322709
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|33679011|gb|CF307250.1|CF307250
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|88579491|gb|CI688488.1|CI688488
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
EST: gi|66924401|gb|CX111249.1|CX111249
EST:     CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAA                         ATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT
genomic: CTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttcttt ... tcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgtttacatattgctctgtctaattattcctactctcataatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG
                     gtctaat  putative branch site (score: 3)
                                             tcttcacc  putative PPT
      tttacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttctttctttctttaccaatctcatatttgtgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgtttacatattgctctgtctaattattcctactctcataatcttcaccagATGGCTGAGTATAGAATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA