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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC

Basic information

species Oryza sativa
transcript LOC_Os06g03970.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G082855_T05 (Zea mays), 3'ss of exon 23
gtaagccaccccacttccacagttccactccatcctctcatcacattgtgcaaaattatcaccaattctagaacttttctagcatgatc-caatggatgatt-tgtatgacaagatcttgtgtcaatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC
                                   |||  |  | | | ||    || |  |     || |  |   |  |  |||  |  || | |||  | ||   ||  | |||        | ||  |||||||||| || || || ||| |||| || |||||||| |||||| |||||||||| ||||||||||||||||||   |||||  |||||||||||||||
------------------------tggaaatggtgtctggtttcttggagcggttttttttcg---ccttgcgcgagtagattatggccgtaacgcatgtctctgctggattaaatcac------acgtgtagATACTCTCGAAGGCCGACGACGACACGGTGATGGAGGCCGTGGACCCGGAGGTGTCGGTGACGTGCACGGACATGAACCTGGTGCGGAAGGCCTTCCAGC

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 25
-------------------gtaagccaccccacttccacagt--tccactccatcctctcatcacattgtgcaaaattatca---------ccaattc--tagaac-----ttttctagcatgatccaatggatgat--ttgtatgacaagatcttgt--------gtca-atgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC------------
                    |   |    ||| ||  | | |  ||  | |   |     |  | ||  || |  || ||           |   ||   | || |     ||||    | ||  | | | ||| ||    |||   || |    ||          ||| | ||  |||||||||| || || || ||| |||| || |||||||| |||||| |||||||||| ||||||||||||||||||   |||||  |||||||||||||||            
gtgagtccccagatcatcctttgactctgccatttttatactggtcatcacggcctagctagtagatgctgaaggatgatggaaatggtgtctggtttcttggagcggttttttttcgccttgcgcgagtagattatggccgtaacgcatgtctctgctggattaaatcacacgtgtagatactctcgaagGCCGACGACGACACGGTGATGGAGGCCGTGGACCCGGAGGTGTCGGTGACGTGCACGGACATGAACCTGGTGCGGAAGGCCTTCCAGCTCGCGCTGCTGT

upper sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G082855_T04 (Zea mays), 3'ss of exon 24
-----------------------gtaagccaccccacttccacagt--tccactccatcctctcatcacattgtgcaaaattatca---------ccaattc--tagaac-----ttttctagcatgatccaatggatgat--ttgtatgacaagatcttgt--------gtca-atgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC
                        |   |    ||| ||  | | |  ||  | |   |     |  | ||  || |  || ||           |   ||   | || |     ||||    | ||  | | | ||| ||    |||   || |    ||          ||| | ||  |||||||||| || || || ||| |||| || |||||||| |||||| |||||||||| ||||||||||||||||||   |||||  |||||||||||||||
gtgagtgagtccccagatcatcctttgactctgccatttttatactggtcatcacggcctagctagtagatgctgaaggatgatggaaatggtgtctggtttcttggagcggttttttttcgccttgcgcgagtagattatggccgtaacgcatgtctctgctggattaaatcacacgtgtagATACTCTCGAAGGCCGACGACGACACGGTGATGGAGGCCGTGGACCCGGAGGTGTCGGTGACGTGCACGGACATGAACCTGGTGCGGAAGGCCTTCCAGC

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|86479702|gb|CI122335.1|CI122335
EST:     TGCTCACAGGGAAGAAGCCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|58668197|gb|CK056883.1|CK056883
EST:     CGACAACGAATCGAACTTGCATCAAGTTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGA
genomic: CGACAACGAATCGAACTTGCATCAA-TTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGA
EST: gi|163926182|gb|EG711834.1|EG711834
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|38482930|gb|CF966732.1|CF966732
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACGGCACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|2317603|gb|C22657.1|C22657
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATANTCTCCAAAGCTGATG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATG
EST: gi|38479012|gb|CF963145.1|CF963145
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAGAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|66923246|gb|CX110094.1|CX110094
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|2317602|gb|C22656.1|C22656
EST:     AAGAA-GCCCTCG-CAACGAATCGAACTTGCATCAATTG                         -TACTCTCCAAAGCTGATG-CCACACAGTCATGGAGGCATTGGCCTCGGAG
genomic: AAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|38477005|gb|CF961138.1|CF961138
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAG
EST: gi|58661800|gb|CK050480.1|CK050480
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGC
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGC
EST: gi|38477623|gb|CF961756.1|CF961756
EST:     TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTG                         ATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGT
genomic: TGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGT

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: 63 (upstream exon), 57 (downstream exon)
Score: 9

GCTCAATGAGAAATCTGATGTGTACAGCTTCGGCATCGTCCTTCTGGAATTGCTCACAGGGAAGAAGGCCGTCGACAACGAATCGAACTTGCATCAATTGgtaagccacc ... caatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctagcatgatccaatggatgatttgtatgacaagatcttgtgtcaatgttcagATACTCTCCAAAGCTGATGACAACACAGTCATGGAGGCAGTGGACTCGGAGGTGTCAGTGACGTGCACGGACATGGGACTGGTCAGGAAGGCCTTCCAGC
                      atttgtat  TA-rich tract