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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
gta-gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
||| | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  |||||||   | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtccaa--ctcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                           | || | || |  |   |  ||||    || |||      |  || |||||   |  |   | |  |  ||  | |  |  |   | ||  || |     ||| ||||  | || || ||    |   |  | ||| |||| ||  | |||||||| |||||||||||||| |||||||| ||||| ||||  || ||
-------------------------------------------atttta-gtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttag--cgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                             ||  ||| |  |   |  ||||    || |||      |  || |||||   |  |   | |  |  |||  |    | ||  ||||  || |     ||| ||||  | || || ||    |   | || ||| |||||||  | |||||||| |||||||||||||| |||||||| ||||| ||||  || ||
--------------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                        ||| | |    |     | |     |    ||      | |||   |||      |      |  ||    |     | | ||     |||||   || || |||||  | || || ||   || || ||| |||||||||||| | |||||||| |||||||||||||| |||||||| || || ||||  || ||
---------------------------------------catggccttcactaccactgattaggaattgattcttaagtcatgcaatattacttaatattgctcatttgtagactaatagtt-----catttgacat-atacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttg-atcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                             ||| |  |||   ||    |||   |      |     ||   |||    |  | |||  | || || |     || ||    |  |||||    ||  ||||| | || || ||    |||||||| |||||||| ||| | || ||||| ||||||||||||||||||||||| || || || |  |  ||
---------------------------------------------ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttcta-cttgaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG

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|2310581|gb|C26736.1|C26736
EST:     GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|2310581|gb|C26736.1|C26736
EST:     GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|2310581|gb|C26736.1|C26736
EST:     GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GTGATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GTGATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GTGATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGG                         T
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-Ggtagttgtac ... tatcatgcag-
EST: gi|33796287|gb|CF324010.1|CF324010
EST:     GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTG                         GTAGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATAT
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGgtagttgtac ... tatcatgcagGT--T-GCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATAT
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     GTGATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTG                         GTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
genomic: GTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGgtagttgtac ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA

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: 70 (upstream exon), 65 (downstream exon)
Score: 6

GGGTCTTCTTCCAAATGGTGGATGTTCAGACAAGTCCAGTTTCTTGAACAGTGACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGgtagttgtac ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                             aattgac  putative branch site (score: 6)
                                        tttcttatc  putative PPT
                                       atttcttat  TA-rich tract