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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccctttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
-----------------gtaaagtttctact-atctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccct-ttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
                   |||  | ||| |    || | | | | |   ||   || |  ||    || || | ||  ||   | |      | |||| ||   |||||||||||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| || ||
gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
---------gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtca-----tgattggatgatcccct-ttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
          ||||     |||||| | ||| || ||||| |   |   |     || || |||     | |   ||   | |      |||||| ||   |||||||||||| ||||||||||||||||| ||| |||||||||| |||||||| |||||||| || ||
gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 7
------------------------gtaaagtttctactatctactttgtattttggcac--at-atagtacatactaagtcatgattggatgatcccctttttgccaacttgc-agATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
                        ||    ||| |  | |  |||     |||  |||   || ||  |   ||| | |     ||| | | ||   ||     ||  | | | |||||||||||| |||||||| |||||||| ||||| ||  | |||| ||||||||| || ||  | ||
gtgagtatctgattgggactaatggtgtcatttatgttcttcactaatgctttctgcattgatgatgatgagtaccatgctgccatttgtttattaactcccccccccccttctagATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------gtaaagtttctactatctactttgtattttggcacat--atagtacatactaagtcatgattggatgatcccctttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
                                                                || ||| |  || ||  | ||  | |  ||    ||  ||   |  |  | ||| |  ||  | | | |   ||||| |  |  ||||||||||||||| |||||||| |||||||| ||| |||| || || | |||||| || || ||  | ||
gtaagcatctgatattgaataattgccatttatggtgacttatgttttccaaaagattgtggtctagagtctagacaatgcatttcttgtagtgatgaattaatgacaagtgttgagt-actataagtttaacattttttttc--atctgcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------gtaaagtttctactatctactttgtattttggcacat--atagtacatactaagtcatgattggatgatcccctttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
                                                                || ||| |  || ||  | |   | |  ||    ||  ||   |  |  | | |  ||  |  ||    |  ||||     |  ||||||||||||||| |||||||| |||||||| ||| |||| || || | |||||| || |||||  | ||
gtgagcatctgatgttgaataattttcatttatggtgacttatgttttccaaaagattatggtctagagtctagacaatgcattccttgtagtgatgaattgatgacaagtgttgaatactg--tacatttatcttttttgtttcatctgcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
-gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccc--tttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
  ||   || | | |||     |   |          | ||  | |  |||   |     |  |  ||      ||||       || ||||||||||||| |||||||| || ||||| ||||||||| | ||||  ||||| ||||||||  | ||
gttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG

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|58660884|gb|CK049564.1|CK049564
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|24208295|gb|AU225322.1|AU225322
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|163923153|gb|EG709322.1|EG709322
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|88256807|gb|CI354588.1|CI354588
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|33797218|gb|CF324473.1|CF324473
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|88664333|gb|CI687436.1|CI687436
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
EST: gi|58675617|gb|CK064304.1|CK064304
EST:     CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTG                         ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC
genomic: CCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgtaaagtttc ... caacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatagtacatactaagtcatgattggatgatcccctttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
                                 tcccctttttgcc  CT-rich tract
           atactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccctttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT