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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttttattttgtaatcttgtccttctctctgtactaatacattttatttcccatgttagcacgtcactcatatatctccctaatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G125310_T01 (Zea mays), 3'ss of exon 5
gtatgtgtttttattttgtaatcttgtccttctctctgtactaatacattttatttcccatgttagcacgtcactcatatatctccctaatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG
||  || || |||    |||   |||| |    | ||    |||||  ||  ||       || | || |  | | || || | |  |    |||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||
gtgagtcttgttaccccgtatctttgtgcgatgcacttctttaatagcttgaatg------gtcatcaggaaattaat-taacactttgtacctgtagCAACTGGGGCACGGAAAATGACCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtgtttttattttgtaatcttgtccttctctctgtactaatacattttatttcccatgttagcacgtcactcatatatctccctaatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG
               |   || |   | ||  || || ||||    |  |||  || |   | | | || |  || | ||||     | |   || ||||||||||| ||||| | ||||||||| || |||||||| || ||||||||||| || |||||||| ||||
--------------gtaagaaacaaatactaatccct-tactttctctctttcctttcttggattgaacatttcttacatatgaattttac-ttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG

upper sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0061g00460.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtgtttttattt--tgtaatcttgtccttctctctgtactaatacattttattt-------cccatgttagcacgtcactcatatatctccctaatactgt---agCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG
|||    || | ||||  | | || |  ||  | |||    |  |||   | |   ||       || |  || ||     ||   ||    |||  || | |||   ||||||||||| || || | ||||||||| |||||||||||||| |||||||||||||| |||||||| ||||
gtaacaattatcatttattttgatgtcctctctatctgcaaaacaatctttctggcttacccatccctagttttgctgacaacgtgtaatgttccaaaaaattgttacagCAACTGGGGTACTGAGAGTGATCCTGACTTCAAAGGTTACCACAATGGGAACTCAGAACCTCGTGGATTTG

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|33818513|gb|CF335087.1|CF335087
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|38478143|gb|CF962276.1|CF962276
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTAGCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|87026661|gb|CI254767.1|CI254767
EST:     AGAGGACTGTTTGGACTTTTGGGCAAA-GGCNTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AGAGGACTGTTTGGACTTTTGGGCAAAGGGC-TACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|38482501|gb|CF966535.1|CF966535
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|87034760|gb|CI189384.1|CI189384
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGACCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33819105|gb|CF335377.1|CF335377
EST:     GACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: GACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|86599770|gb|CI255932.1|CI255932
EST:     AAGAGGACTGTTTGGGCTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     AAGAGGGCTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|86536276|gb|CI176482.1|CI176482
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33813841|gb|CF332806.1|CF332806
EST:     GAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: GAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|86496472|gb|CI139105.1|CI139105
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|88575843|gb|CI669988.1|CI669988
EST:     AAGAGGACTGTCTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCANACA                         CAACTGGGGCACAGAAAATG
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATG
EST: gi|58588133|gb|CF986441.1|CF986441
EST:     ACGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|86593628|gb|CI264507.1|CI264507
EST:     GGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: GGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: AAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|86511468|gb|CI154101.1|CI154101
EST:     GGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: GGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
EST: gi|33815682|gb|CF333692.1|CF333692
EST:     ACACTTGAGCTCACACA                         CAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA
genomic: ACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAA

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: 61 (upstream exon), 62 (downstream exon)
Score: 62

GATGTGGAATCGGCCCCTACTGATCCTGTAAAGAGGACTGTTTGGACTTTTGGGCAAAGGGCTACACTTGAGCTCACACAgtatgtgttt ... aatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacattttatttcccatgttagcacgtcactcatatatctccctaatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG
                                      tctcccta  CT-rich tract
     ttttattt  TA-rich tract