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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_Os10g11140.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttcactatcttttttaattttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
                       ttctaat  putative branch site (score: 2)
                                              ttctgtt  putative PPT
       actatcttttttaatt  TA-rich tract