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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_Os03g07570.1
intron # 7
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

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), 75 (downstream exon)
Score: 122

AGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttcct ... tgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatactaataaagccctgttaacactttgcctcttcatccttgtaatccagATCTCAACATTTTAGTTGGAAAAGGTGGTCTGCATGGTAATGTCTTCAGGATAAAACCACCAATGTGCTTTACAAGGGATGATGCAG
                            ctttgcctcttcatcc  CT-rich tract
     atactaataaa  TA-rich tract