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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA

Basic information

species Oryza sativa
transcript LOC_Os06g44150.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 4
gtaaatcagcatctctcttaccctc-atcc---atactgccatca---cctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
|||   |||||| | |  | | ||| || |   |||     ||||     | | |||    || ||    || || |   |||||||||  |     ||   | || |   |||||||||| |||||||| |||||||| || ||| |  | || || || |||||||||||||| |||||||| |||||||||||||||||||| |||||||
gtatgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgt-aacttatttgac----tttccatatgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G170326_T01 (Zea mays), 3'ss of exon 5
gtaaatcagcatctctcttaccctcatccatactgccat-cacctcttcatcctgcata--caatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
|||  ||  ||| | |  ||| ||  |   |   |  || ||  ||    |  |||||   | ||    ||   |    ||||||  | ||  ||   | || |   ||||||| || |||||||| |||||||| || ||  |  | || || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||
gtacgtcgacatattttatactctgcttatttgggatatgcatatcaggtttatgcatttcccatactgctggtctgtgttatttgacttgagttccatatgttcctagGACAACGTGCGGAACCAGCTGATCCAGTTTGAGTTGCTCCTAACGACTGCAACATTTGTTGTGGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 5
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatac--aatgggcctataccaacttattttccatggctt--tgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
      |  ||| | | |||         |||  |  ||      || | | ||  ||    |  |   |||   || |||       || |    | || | ||  ||||| ||||| || || || || || || || || |||||||||||||||||||||||||| || ||||| ||||||||||| || || |||||||||||||
------cttcatttgtattatgt--gatgatatgg--attgttcattgaacttgtttatctgactgaattattttaatttagaacagctgaccgaatatttttctcacagGATAATGTGCGAAATCAGCTTATTCAGTTTGAGCTTTTACTCACAACTGCAACATTTGTGGTTGCCATCTTTGGAGTGGTAGCAGGAATATTTGGGATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 5
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcata--caatgggcctataccaacttattttccatggc----tttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
          || | | |||         |||  |  ||      |  | | ||  ||    |  |   |||   || |||   |   || |    ||| || | ||  ||||| ||||| || || || || || || || || |||||||||||||||||||||||||| || ||||| ||||||||||| || || |||||||||||||
----------atttgtattatatgtgatgatatgg--attgttcatggaacttgtttagctgactgaattattttaatttagaatagctgaccgattttttttttctcacagGATAATGTGCGAAATCAGCTTATTCAGTTTGAGCTTTTACTCACAACTGCAACATTTGTGGTTGCCATCTTTGGAGTGGTAGCAGGAATATTTGGGATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatcagcatctctct-taccctcatccata-ctgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
       |  | |||    | || || |||| | |||  || |  ||   ||   | || ||   |    || |  |     | | ||           |   | ||||| ||||| ||||| || |||||||| |||||  |  | || || |||||||| |||||||| ||||| ||||| || ||||||||||| ||||||||||
-----gtaatacctcaaaattccatcttccacagctgatattaa-tccagattgagaatgcacaagagtcatgctgaaaacctcttca----------atatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 4
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatggct-ttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
     | ||  ||  | ||| |  |||    || |||||   |  |   |     ||    ||  | | ||   |   |||   | |   | || || ||||  ||||| ||||| || ||||| ||||||||||| || ||  |||||||||| ||||| |||||||| ||||| ||||| || || || || |||||||| ||||
-----tgagtgtccattttatca-cattggaacagccatggtca-tgattttcatattgtttgatcttttagagagacattagacgtatttgttattttgctcacagGATAATGTCCGAAACCAGCTGATCCAATTTGAGCTACTACTCACAACAGCAACTTTTGTTGTTGCCATCTTTGGGGTTGTAGCAGGCATATTTGGTATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S423_14V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatacaatgggcctataccaacttattttcc--atggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
   | |   | | |   |||   |  |    | |   |||  | | |  |  || | |  |||   |  | | || || | |  |  |||| | |||| |     ||||||||||| ||||| || ||||||||||| || ||||| |||||||| |||||||||||  | ||||| | | | ||||| || ||  | ||||| ||||
---atttttctttttctttattttttttttgaatttaatctgcacgtactagtgaagaagatg---cagtgctaatttttgtggctgatgggtatgtttt--caacagGACAATGTGCGGAATCAGCTGATCCAATTTGAGCTTTTGCTCACAACAGCAACATTTGTGTTGGCCATCTATAGTGTGGTGGCAGGTGTGTTTGGAATGA

upper sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S493_8V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatg-gctttgttgtgcttt--cagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
       |   ||  ||||||  ||  |  | |    |    ||   | |    ||||||     |  ||     || |||||    | | |  |   |  ||   ||||||||||| ||||| || ||||| ||||| || ||||| || ||||| |||||||||||  | ||||| |   | ||||| || ||  | ||||| ||||
-------aatctccatcttacaatcgac--ttcgtataggttctggacgtagaacatacatgttactcatcatcgctaattttgtgggcgatgggaaatatttgaacagGACAATGTGCGGAATCAGCTGATTCAATTTGAGCTTTTGCTTACAACGGCAACATTTGTCTTGGCCATCTACAGTGTGGTGGCAGGCGTGTTTGGAATGA

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|88530864|gb|CI459290.1|CI459290
EST:     ACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: ACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|88223841|gb|CI223690.1|CI223690
EST:     CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|88384346|gb|CI551272.1|CI551272
EST:     ACATTGATGACAGTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: ACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|86492625|gb|CI135258.1|CI135258
EST:     CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|88524411|gb|CI452321.1|CI452321
EST:     TGACACTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: TGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|86535033|gb|CI175239.1|CI175239
EST:     CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|88961904|gb|CI097057.1|CI097057
EST:     CTGAAGGAGTACATTGATGACACTGAAGATTTGATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
EST: gi|88249989|gb|CI249838.1|CI249838
EST:     CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG                         GACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA
genomic: CTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTGgtaaatcagc ... gtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
                                              tgctttc  CT-rich tract
                      aacttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcagcatctctcttaccctcatccatactgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG