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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG

Basic information

species Oryza sativa
transcript LOC_Os08g42370.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagaca---tgtgcgtatt------------tgtttggagttattcttccagtgc---ttttcatt-----gagctct-------cttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
|||||| | | | | ||| ||| | |||||| ||| | | | ||||| || ||||||||| || |||| | | | |||||||| || | | ||| || || ||||| ||||| || |||||||| ||||||||||||||||||||||||| ||||||||||||||||| || || ||||||||||| |||||||| |||||||||||||| | |||||||||||| ||
gtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaa-catatttg-tgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
gtaagtatcatgttttt-ccagcagttctgtacctatccttaccgta---ggaaagacatgt-gcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
|||||| || || | || ||| || |||| | || | | || || | | | | ||| | || || || | | | || ||| || || || || | ||| || |||||| ||||||||||||||||||||||||| |||||||||| |||||| || || |||||||| || |||||||| |||||||||||||| | |||||||||||| |
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttct----attttgttaagactgaccatcaa-tgtatttg-tgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgct-tttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
|| || | | | || || | || | | ||| | | ||| || | || | | || || | || | | |||||||||||||||| ||||||| ||||||||| ||||| || || |||| || | || || || || || |||||||| || || | | |||| | |
------------------------------------------------aattgtatatatatttctggtttg-gtgacttttcagttattattttatacatgtcattcttgaatgttatgtatctgaattgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgt-atttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgag---cctaatca-taaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTT--GCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
||| | | | |||| ||| | || ||| | || || | |||| || | || | |||||| | | ||| |||||||||||||||||||||| | ||||||||| ||||| || ||| || | || | ||| | ||| || || || ||||| || || | | ||||
-----------------------------------------------------cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC--

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgct-tttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttg--gtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
| || | | | || || | || | | ||| | | ||| || | || || | || || | | ||| | ||| |||||||||||||||| ||||||| ||||||||| ||||| || || |||| || | || || || || || |||||||| || || | | |||| | |
-------------------------------------------------attgtatatatatttctggtttg-gtgacttttcagttattatttgatacatgtcactcttgaatgttatgtatctgaatgtgt-gcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatca-taaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTA-GAAATG
||| || || | || || || | | | ||| | | || ||||| | | | | | |||||| | | ||| |||||||||||||||||||||||| ||||||||| ||||| || ||| |||| || | || || ||||| || || ||||| || || | | |||| | ||
-------------------------------attattttttttgt----------tctgtttacttttcagttatcatttgctatgcattatt-attgaatatacattatgt-------atcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTGTGTATATATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGCAT-

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTA-GAAATG
| | | | | || || || | | ||| |||| | | |||| | | | || | | | | | | || ||| |||||||||||||||||||||||| ||||||||| ||||| || ||| |||| || | || || ||||| || || ||||| ||||| | | |||| | ||
------------------------------------------aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatcc-ttgaatatgcattatg-catcctaattg----cttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT-

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
| || | | | | || | ||| | || | | |||||| ||| | | | | || || ||| | ||| | || | |||||||||||||||||| || |||| ||||||||| |||||||| || | || || | || || |||| ||||| ||||| || || | | ||| | ||
---------------------------------------ttttccagttgtcatcttcaccaacatgataggaatgatgcat---gtgcttgaatttgtgggcaatgc--atgaatctgaacactttcaca----attctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT

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|88327636|gb|CI646829.1|CI646829
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCT
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCT
EST: gi|29666673|gb|CB662948.1|CB662948
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|25802931|gb|CA758892.1|CA758892
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACTACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|88301943|gb|CI667789.1|CI667789
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|29672455|gb|CB668730.1|CB668730
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC

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: 75 (upstream exon), 74 (downstream exon)
Score: 84

GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                           gcctaat  putative branch site (score: 84)
 taatcataaa  TA-rich tract