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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatataatccttataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG

Basic information

species Oryza sativa
transcript LOC_Os01g67126.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 5
gtacaaatataatcc--ttataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
||| |||| |       ||   || || ||  |   |    |||   ||||   |   ||    ||| |  || | ||  |||||||||||| ||||||| || |||||| ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||
gta-aaatttggctaaatttcgatcttattttttgctgatgtcacattggttgggcatttatattgtttcttttcgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 5
gtacaaatataatc---cttataatttttttactctatatgctcatgc--tggtcttgatcttgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
||| |||| |   |     |||||| || ||    ||| || |  |||  |||| | |   ||   | |  |  ||   ||  |||||||||||| ||||||| || |||||| ||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| || || || |||||||
gta-aaatttggccaaatatataatcttattttaatatctgatgttgcattggtttggtatttctgacggttctttttgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 5
-----------------gtacaaatataatccttataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgat----tcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
                  |  |||| || ||    |  | |||||  |    ||  |  |   |||    |  |    || | ||||    | || |  |||||||||||| ||||||| || ||| || ||||| || || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||
gtaaaattaaaacaaatatttaaatttattctgcttgctgtttttttttgtgatattgctttgggtgaacaattgagcatttgtgatgattttctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 5
gtacaaatataatccttataatttttttactcta---------tatgctcatgctggtcttgatcttgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
|||   ||        |||   |||| | | | |         | |  |   ||||     | |  |||  |||||  |   |||  |||||| ||||| ||||| || |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || || || |||||||
gtatttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 5
gtacaaatataatccttataatttttttactcta-----tatgctcatgctggtcttg--atct--tgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
|||   ||    |   |||  | ||| | | | |     |    |  |  |||   ||  | ||  |||  |||||  |   |||  |||||| ||||| ||||| || |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || || || |||||||
gtatttatgagtttgctatgctgtttgtgccccagcgagtgcctttcttttggctgtgtaagctaatgagttgtatcttattttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 5
gtacaaatataatccttataatttttttactctatatgctcatgctgg-----tcttgatcttgatatgta--tgatt-----cctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
|||   ||  | |   |||  | | | |  | | | |||   |||||      |||   | ||| ||  ||  || ||     | |||  |||||| ||||| |||||||| |  || ||||| |||||    |||||||| |||||||||||| | |||||||| || |||||||| || ||||| |||||||
gtatttatgaatttgctatgctgtgtgtg-tgtgtgtgcaactgctgcctttctctcagttttgttaattaattggttgtatccttttcatcagGCTACTGGAGAGGACTATTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTG

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 5
gtacaaatataatcctt-ataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgattcctttgg----------tcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
|||    | | ||| || ||    | || |   || |    | ||   || || |||||   ||  || | |   |             |||||||||||| |||||||  | ||| |||||| |||||   || || ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||
gtatgt-tgtgatcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcagGCCACTGGAGAGGACTTTTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTG

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|218499062|gb|FG952648.1|FG952648
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCA-GAGTACGA-GGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGAGAGGCCTTT
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAG-GAGGCCTTT
EST: gi|58688294|gb|CK076981.1|CK076981
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|2443100|gb|C74871.1|C74871
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|33794896|gb|CF323328.1|CF323328
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|55410467|gb|CV722843.1|CV722843
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|218483963|gb|FG953648.1|FG953648
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|218499324|gb|FG966003.1|FG966003
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCTTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|396941604|gb|HO188261.1|HO188261
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|86898441|gb|CI292329.1|CI292329
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|4879230|gb|AU063529.1|AU063529
EST:     GGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|218497228|gb|FG948508.1|FG948508
EST:     GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC
EST: gi|163927771|gb|EG712507.1|EG712507
EST:     GTGTGCTCAAGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATATTGAG                         GCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGCGGCCTTTC
genomic: GTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTC

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), 72 (downstream exon)
Score: 168

CTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatat ... ctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactctatatgctcatgctggtcttgatcttgatatgtatgattcctttggtcagGCCACTGGGGAGGACTACTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTG
                           tcttgat  putative branch site (score: 168)
                                          ttccttt  putative PPT
                                atatgtat  TA-rich tract