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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttacaccttttttcattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG

Basic information

species Oryza sativa
transcript LOC_Os10g11140.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
gtatgttttacaccttttttca-ttcattgtgtgcttcactatcttttttaa-------ttttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
||||| |||  | ||| | | | || ||| ||||  | ||||||   |||         |||| || ||   |   ||||  |  | | |||||||||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| |||||||| |||
gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
----------------gtatgttttacacctttttt-cattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttc--aattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
                 | | |  |  |   ||||  |||  |  |   || | ||  |      | | || ||  ||  ||    ||| |  |||| |   |||| |||||||| || || |||||||||||||||||||| || || || ||  ||||||||||||| |||
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 6
----------------gtatgttttacacctttttt-cattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttc---aattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
                 | | |  |  |   ||||  |||  |  |    | | ||  |      | | || ||  ||  ||    ||| |   |||| |   |||| |||||||| || || |||||||||||||||||||| || || || ||  ||||||||||||| |||
gcatgccagttagagtttttctcctggagtattttgacatatagggataacataacctttccagctcacttgctcctttcttctgatttcctcaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgttttacaccttttttcattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
| | | |||  |  || | ||  |  ||      ||||  ||| |||||   ||  | | || |||  | |    |||||   |||| ||||| || ||||| |||||||||||||||||||| ||||| || ||  |||| ||||||||||||
gcaagctttttaatttatatc--ttcttacaaagttcaagatcgttttt---ttcattactc-ttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------gtatgttttacaccttttttcattcattgtgtgcttcactatcttttttaattttctaattca-ttgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
                                  |   | |  |||||| ||| |   | |   | ||   ||  ||| ||   |||| |||  || ||  |       | | | | |||||||||| || || || |||||||||||||||||||| |||||||| ||  |||||||||| ||||||
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttatttta---aatccatactcatctgccttgttc--ttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG

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|58608460|gb|CK036493.1|CK036493
EST:     ACGGTCTGCTGTCAACGCCTGCTGTATCTGCAGTAATTCGTAAAAGACAA                         GCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGAT
genomic: ACGGTCTGCTGTCAACGCCTGCTGTATCTGCAGTAATTCGTAAAAGACAAgtatgtttta ... attctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGAT
EST: gi|29681950|gb|CB678225.1|CB678225
EST:     ACGGTCTGCTGTCAACGCCTGCTGTATCTGCAGTAATTCGTAAAAGACAA                         GCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGAT
genomic: ACGGTCTGCTGTCAACGCCTGCTGTATCTGCAGTAATTCGTAAAAGACAAgtatgtttta ... attctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGAT

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), 70 (downstream exon)
Score: 56

GAACGGTCTGCTGTCAACGCCTGCTGTATCTGCAGTAATTCGTAAAAGACAAgtatgtttta ... attctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttcactatcttttttaattttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
                       ttctaat  putative branch site (score: 56)
                                              ttctgtt  putative PPT
       actatcttttttaatt  TA-rich tract