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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_Os05g38150.2
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|86851167|gb|CI312568.1|CI312568
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|89187311|gb|CI047378.1|CI047378
EST:     GTCACTACAGATGATAAGTTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|86431434|gb|CI085045.1|CI085045
EST:     GCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|66915778|gb|CX102626.1|CX102626
EST:     GTCACTACAGATGAT-AGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|25798187|gb|CA754084.1|CA754084
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|88262625|gb|CI366399.1|CI366399
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAACTACGAGATTCTCTTATGGGGCTCCTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|163917821|gb|EG712147.1|EG712147
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|89178281|gb|CI391460.1|CI391460
EST:     CAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCCTTT
genomic: CAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
EST: gi|87029670|gb|CI257465.1|CI257465
EST:     GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAG                         TGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT
genomic: GTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 68 (downstream exon)
Score: 34

TGCTCATACAGATTGTATCGTCACTACAGATGATAAGGTAGCAGAGACTTTTCTACGCAGAGTTGATAGgtatgtttaa ... atttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
                    aactaat  putative branch site (score: 34)
                 tttaactaat  TA-rich tract