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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttccttattccttttctcttttccatgatcgcatcattattagtttatactaataaagccctgttaacactttgcctcttcatccttgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g07570.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g07570.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 7
---gtgctttccttattccttttctcttttccatgatcgc--atcattattagtttatactaataaagccctgttaacactttgcctcttcatccttgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG
     |  |  | | || | |    | |  |||||||     ||  |||||  | | ||||    | | | | ||     ||||| || | || ||||| | | |||||||    |  |||||||||| || |||||||||||||| |||||||| ||||||||||| ||||||||| | | ||| |||||||
gtgccgtctctcatttttcctgctccatgaccatgattatttatatttattgatctctacttgccatgacatttttgttttttgcttcataatacttgttaac-agATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAATAAAACCACCGATGTGCTTTTCGAAGGACGATGCAG

upper sequence: LOC_Os03g07570.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
gtgctttccttattccttttctcttttccatgatcgcatcattattagtttatactaataaagccctgttaacactttgc--ctcttcatccttgtaa--tccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG
          ||     |||   |     |  |      |||    || ||    |   |||        || || | |   || || |  | | |||  |  ||| |||   ||| ||||||||||||| || |||||||| ||||| || ||||| || ||||||||||| || || |  ||||||||||
---------gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG

upper sequence: LOC_Os03g07570.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G36000.2 (Glycine max), 3'ss of exon 7
gtgctttccttattccttttctcttttccatgatcgcatcattattagtttatactaataaagccctgttaacactttgc--ctcttcatccttgtaa--tccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG-------------
          ||     |||   |     |  |      |||    || ||    |   |||        || || | |   || || |  | | |||  |  ||| |||   ||| ||||||||||||| || |||||||| ||||| || ||||| || ||||||||||| || || |  ||||||||||             
---------gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAGGTATATAAATAAA

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|27553979|gb|CA997879.1|CA997879
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|86433407|gb|CI093750.1|CI093750
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|86489526|gb|CI132159.1|CI132159
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|88901607|gb|CI001715.1|CI001715
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|116875647|gb|EC366155.1|EC366155
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|29688224|gb|CB684499.1|CB684499
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|38473892|gb|CF958024.1|CF958024
EST:     GAAGACACCTGCCAATGCCGAGACCAATTTATTGTTTGAGAAACTCAATG                         ATCTCAACATTTTAGTTGGAAGAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|27578133|gb|CB000828.1|CB000828
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|89163358|gb|CI100248.1|CI100248
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCGTGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|88993673|gb|CI112577.1|CI112577
EST:     CCTGCCAAGTCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: CCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|86519627|gb|CI159833.1|CI159833
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|29636945|gb|CB641954.1|CB641954
EST:     GAAGACACTTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|89187693|gb|CI115139.1|CI115139
EST:     GAAGACACCTGCCAAGNCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|86497504|gb|CI140137.1|CI140137
EST:     GAAGACACCTGCCAAGNCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|88223750|gb|CI223599.1|CI223599
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|87015740|gb|CI277698.1|CI277698
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|88834152|gb|CI000516.1|CI000516
EST:     GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|89181642|gb|CI113148.1|CI113148
EST:     CCAAGTCCGAGACCTATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: CCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA
EST: gi|14571325|gb|BI118693.1|BI118693
EST:     GAARACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGG                         ATCTCAACATTTTAGTTGGAAAARGTGGTCTGCATGGTAATGTCTTCAGGA
genomic: GAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatactaataaagccctgttaacactttgcctcttcatccttgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG
                            ctttgcctcttcatcc  CT-rich tract
     atactaataaa  TA-rich tract