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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os05g38150.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G061777_T01 (Zea mays), 3'ss of exon 2
gtatgtttaaacattaa----ttcccttattact------taatggttac-------atta-------tttgttcc--ctattgatgcacaat--tattttcctgtcaactta-tgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
||| |||||||||| |     | | ||| ||| |      || || ||         ||||       ||| |||   || |   ||| | ||  | ||||  | | || | | ||||||   ||| | | ||| ||| | | || | ||   |||||  |||||||||||||| |||||||||||||| ||  |||||||||| |||||||||||||||||||||||||||
gtacgtttaaacatcagcacctcctctttttattcatttttactgtttgtgcaatcaattaaatgtgttttattcttgctgtcactgcgcgatgttcttttgttctgaattcaatgatga-tagatatctcactgatggtatatttttcta--caattgcaacagTGCTGCTGTGTTTCATAATGCAAGCACACGATTCTCTGACGGGGCTCGTTTTGGATTGGGTGCTGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
-------------------------gtatgtttaaac-attaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttct-caatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                          |   |||  ||  ||  | |  |   |   |||  ||    |  ||||  | | | || || |||||  | ||    |     |   ||||   |||   || || ||||| | ||  |||||| |||||  |||||||||||||||||||||||||| |||||  |||||||||||||||||||||||||||||||||| |||
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactg-tgtacaatgttattttgtttggagttcaatgat--gattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G061777_T03 (Zea mays), 3'ss of exon 2
gtatgtttaaacattaa----ttcccttattact------taatggttac-------atta-------tttgttcc--ctattgatgcacaat--tattttcctgtcaactta-tgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG---------------------------------
||| |||||||||| |     | | ||| ||| |      || || ||         ||||       ||| |||   || |   ||| | ||  | ||||  | | || | | ||||||   ||| | | ||| ||| | | || | ||   |||||  |||||||||||||| |||||||||||||| ||  |||||||||| |||||||||||||||||||||||||||                                 
gtacgtttaaacatcagcacctcctctttttattcatttttactgtttgtgcaatcaattaaatgtgttttattcttgctgtcactgcgcgatgttcttttgttctgaattcaatgatga-tagatatctcactgatggtatatttttcta--caattgcaacagTGCTGCTGTGTTTCATAATGCAAGCACACGATTCTCTGACGGGGCTCGTTTTGGATTGGGTGCTGAGGTAGGTCCTATCTTTTTATATGGCATTTGAGTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 16
-------------------------gtatgtttaaac-attaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttct-caatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG---------------------------------
                          |   |||  ||  ||  | |  |   |   |||  ||    |  ||||  | | | || || |||||  | ||    |     |   ||||   |||   || || ||||| | ||  |||||| |||||  |||||||||||||||||||||||||| |||||  |||||||||||||||||||||||||||||||||| |||                                 
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactg-tgtacaatgttattttgtttggagttcaatgat--gattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAGGTACGCCCTATCTTTGGAGTAAATGGGATTATT

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 14
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctat-tgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                                   ||| | ||   |     || | |||   |  ||||  |      | |    |||||    ||||  | |  ||| | |  || | |||      |  ||||||||||||||||| || ||||||||||| || |||| ||||||  |||| |||||  | ||||| |||
----------------------------------tgtttctttgcataactactctatgaaatatgattaagtctaatactagagttgatg--ttgatgactgaggaatatgcatttttgcttgatt-ctcaaacagTGCTGCTGTATTCCACAATGCAAGTACAAGGTTCTGTGATGGAACTCGCTTTGGCCTTGGTGCAGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgc-acaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                             | ||| |  |  | |||   || | | | |  | |  | ||  | | |||    | ||| | |  |     || | || | | |   | | | |     |   ||||||||||||||||| || |||||||||||| | || | |||||| || || |||||  | ||||| |||
----------------------------ttaaatag--aattcattctctcacaacttagactatgaataact-catgttgcttcatg-tcattg---acttgaata-tatgcgacttttccttgtg-tacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G55610.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgtttaaacattaattcccttat-tacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctactt-ctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
              ||||  || ||| |||| ||     ||||| | || |    |||          ||   |  |   |  |   |||  | ||      ||||||| |  | |  || || |    | |  ||||||||||||| || || |||||||| || ||||||||||||||   | | || ||| | |||||||||
-------------gtaataaccatatatactaaa-----acattttctgctgttgattttccagtccatagaatgtttgtagttg--gatatatgggaa---aactaat-tcttctaatatttgcgtgttctcgacagTGCTGCTGTTTTCCACAATGCAAGCACAAGATTCTCTGATGGTTTTAGGTTCGGACTTGGTGCTGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 17
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                         ||||||       | | | || | |   ||   || | ||||  | ||    |  || | |  |  ||  ||   || | | |  | || | |   |    || |   |||||||||||| ||||| ||||| || || ||||| | ||||||||||||||||||| | || || |||
-------------------------ttactt-----ccagaatgttagctttttaaatatacgcaatgctgttgtctttcacatcttgtttac--attggtagcaagtaatgtggtttgtgt----atattggcagTGCTGCTGTCTTTCACAATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
lower sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctactt-ctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                                 |   | ||||      || || ||| |    |||  | ||| | |    ||  |     |   ||||  |  | |      | || ||| ||  |||||  |||||| ||||||||||||||||| |||||  | || |||||||| |||||||||||  | |||||||||
---------------------------------taccttcattgcgctctctcttttgct-tgtaatactgttcgtattgtattcaggctgtcat-tgttgtaacattaaataatactgcttgcttcatttg--cagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG

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|88261515|gb|CI365091.1|CI365091
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACCAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|87029670|gb|CI257465.1|CI257465
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|86431434|gb|CI085045.1|CI085045
EST:     GCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|25798187|gb|CA754084.1|CA754084
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|163917821|gb|EG712147.1|EG712147
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|66915778|gb|CX102626.1|CX102626
EST:     GTCACTACAGATGAT-AGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|88262625|gb|CI366399.1|CI366399
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAACTACGAGATTCTCTTATGGGGCTCCTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|89178281|gb|CI391460.1|CI391460
EST:     CAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCCTTT
genomic: CAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|89187311|gb|CI047378.1|CI047378
EST:     GTCACTACAGATGATAAGTTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|86851167|gb|CI312568.1|CI312568
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                    aactaat  putative branch site (score: 2)
                 tttaactaat  TA-rich tract