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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG

Basic information

species Oryza sativa
transcript LOC_Os07g37740.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------gtaagtgtgcatcgcattattgttagatgc-taagtaactatggttagatatgcagtttttga--ttcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
                                            ||  | |  ||     |||   || ||   ||  ||  |||   || ||||  |  |||  |  ||     | ||||||| ||    |    |||||  | |  | ||     |  |  | |||     | ||||||        || ||||  |||||| ||||||||||||||||||||| |||||||  | ||||||||||| ||||||||||| ||||||
gtaagctgatcacctttttgtttgctaaatcagatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctttgaaaattttgataaataatcatctagtatccttgatgcgaaac--ataattctatggttcttttggtaacctagtaatccacacgcttgttct--gcagATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G31090.2 (Glycine max), 3'ss of exon 9
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatga-agataat-caacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
                                               || ||||   |||     ||   | | ||| |||| ||      |     || | |||  |    | | | ||  ||          | ||  |  |  ||| | ||| |||| |||||||| |||||||||||||| |||||| | ||| | ||| ||||||| ||||| || |||
----------------------------------------------aatgtgcatccttttgcaaatactacagaatgcaacctaagcaatattctgcttctgaacgattaatcttttattatg----------attttctcca--tttgccttgtagATTTTCTACTTCGTTGGATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
                                       |||  |    || |  ||    || |   |  ||   |||| ||      |     || | |||  |        ||||||| |   | |  | |||  | |   ||| | ||| |||||||||||||  |||||||||||||||||||||| ||| | ||| ||||||| |||||||| |||
---------------------------------------atgcct---catccttttgcaaatactacagaatg--caacctaagcaatattctgcttctgaatga-------ttgatctttt--atta--tgattt-tctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 10
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgt-cggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
|||||| ||| |  | | |    |  ||       |  | | |||  ||   || || |      ||  |  | | ||  |||     || |  | |    ||  ||   | |||| |  |   || |  |  | ||  | |   ||||   || |||| |||||||||||||||||||||||||||||| | ||| ||||| |||| ||||||||||| |||
gtaagtatgcttgtcttgaactatttattaatctcacatgttgtttaattgtcatttgtcacacgatccatgtgaccatttta---agcaaaaccttgttcaatgaaaattctctgcttctaaacgattgataatttactttgcatttttcctgtagATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 12
------gtaagtgt-----gcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattca---tgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctt-------tgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
       | | |||      |  |  | ||||   | |||||   ||| |    || |  |  |  |   ||   ||   | |||  || |    | |  |  | || ||   |    ||||  ||  | || |  |   |    |  ||  | |  || ||          || |||| |||||||||||||||||||||||||||||| | ||| ||||| ||||  |||||||||| |||
gtaagtatgactgtcttgaactacttactattaccacatgctgt-taattgccatttgtcacacgatccatgcgacaattttaagcaaaaccttgtccaatgaaaattccctgcttctaaacgattgataatttacttctttttttttttcttttctttctttccatttacctgtagATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTGTCTGGGTTATTCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
                                                     |   |  |   | |||   |     |  |||   | ||  | ||   ||| |   ||  |   | | | |   |  | | |||| | |  | |||  ||  |||||||||||||  |||| |||||| ||||||| || |||||| ||||||||||||||||||| |||
----------------------------------------------------aaacctaggtgacttgaccttgcatgagatacacatgagg-gtctctagaata---tcgctggaagccttttactggattgattgatttcttcttttattatagATCTTCTACTTCATTGGGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
                                     |  ||   |  |||     |   ||||||||    |       ||   ||     |   |   | || ||   ||   |||| | |         | ||  | ||        |||||||| |||||| || |||||||||||||||||||| | |||||| ||||||| ||||||||| | |||
-------------------------------------ccttgacaaattatt---atcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgg-gatcattt-------acacttcctata--------ttgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

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|86430196|gb|CI082619.1|CI082619
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|3761419|gb|C98667.1|C98667
EST:     GGGGATTTTACCAAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAG
genomic: GGGGATTTTACC-AGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTT-CTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAG
EST: gi|88970336|gb|CI383838.1|CI383838
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|87030942|gb|CI268093.1|CI268093
EST:     GGGGATTTTACCAGCCATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|88225839|gb|CI225755.1|CI225755
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|66923956|gb|CX110804.1|CX110804
EST:     GGGGATTTTGCCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|86429939|gb|CI082362.1|CI082362
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|87027955|gb|CI276311.1|CI276311
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|58683369|gb|CK072056.1|CK072056
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|88969834|gb|CI383336.1|CI383336
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAG
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTT-GTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAG
EST: gi|88966183|gb|CI013059.1|CI013059
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
EST: gi|88834932|gb|CI370235.1|CI370235
EST:     GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGG                         ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC
genomic: GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGC

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), 46 (downstream exon)
Score: 6

GGGGATTTTACCAGCAATTGATCTCATCAGCAAGAATGCTTTGGTGGGGgtaagtgtgc ... ttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
          ttctgat  putative branch site (score: 6)
                                          tttttctttgc  putative PPT
                                     tgtaatttttcttt  TA-rich tract