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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggggactatgttgattcatcttcaaattctgtgttgaaaagcatgctctaagctgagatggctgtggcgttgctgtagcgtgtatgagttgatcttaagttgaatgttggtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG

Basic information

species Oryza sativa
transcript LOC_Os02g40510.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G365688_T01 (Zea mays), 3'ss of exon 2
gtaaaggggactatgttgattcatcttcaaattctgtgttgaaaagcatgctctaagctgagatggctgt-ggcgttgctgtagcgtgtatgagttgatctt-aagttgaatgttggtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG
|||||||| |||||| ||| ||| ||| ||  |||| ||| | |||||||||||| |||||||||   || ||||||| |||| ||    ||| ||  |||| || | || || ||||||||||||||||||||| |  |||||||||||||||||||||| |||||||||| | | || |||||||| || ||||||||||| |||||||| || ||||| ||||
gtaaagggcactatgctgactcacctt-aacctctgcgtttagaagcatgctctaggctgagatgctcgtaggcgttgatgtaccgc-cgtgaattattctttaaatcgagtgctggtgttggcagCTTGGTTTGCCCAAGAAAAACTTCTTCAATGACAACTTCGAGTTGGTGCTCTCAGAACCTAGCGATGCCAATACCAATAGCACCACCCTCCTCTCAGATG

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G145058_T01 (Zea mays), 3'ss of exon 2
gtaaaggggactatgttgattcatcttcaaattctgtgttgaaaagcatgctctaagctgagatggctgt-ggcgttgctgtagcgtgtatgagttgatctt-aagttgaatgttggtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG
|||||||| |||||| ||| ||| ||| ||  |||| ||| | |||||||||||| |||||||||   || || |||| |||| ||    ||| ||  |||| || | || || ||||||||||||||||||||| | ||||||||||||||||||||||| |||||||||| | | || |||||||| || ||||||||||| |||||||| || ||||| || |
gtaaagggcactatgctgactcacctt-aacctctgcgtttagaagcatgctctaggctgagatgctcgtaggtgttgatgtaccgc-cgtgaattattctttaaatcgagtgctggtgttggcagCTTGGTTTGCCCGAGAAAAACTTCTTCAATGACAACTTCGAGTTGGTGCTCTCAGAACCTAGCGATGCCAATACCAATAGCACCACCCTCCTCTCAGACG

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G174083_T01 (Zea mays), 3'ss of exon 1
gtaaaggggactatgttgattcatcttcaaattctgtgttgaaaagcatgctctaagctgagatggctgt-ggcgttgctgtagcgtgtatgagttgatctt-aagttgaatgttggtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG
|||||||| |||||| ||| ||| ||| ||  |||| ||| | |||||||||||| |||||||||   || ||||||| |||| ||    ||| ||  |||| || | || || ||||||||||||||||||||| | ||||||||||||||||||||||| |||||||||| | | || |||||||| || ||||||||||| |||||||| || ||||| || |
gtaaagggcactatgctgactcacctt-aacctctgcgtttagaagcatgctctaggctgagatgctcgtaggcgttgatgtaccgc-cgtgaattattctttaaatcgagtgctggtgttggcagCTTGGTTTGCCCGAGAAAAACTTCTTCAATGACAACTTCGAGTTGGTGCTCTCAGAACCTAGCGATGCCAATACCAATAGCACCACCCTCCTCTCAGACG

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|58589830|gb|CF988138.1|CF988138
EST:     GTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: GTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|58593163|gb|CF991471.1|CF991471
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|29668556|gb|CB664831.1|CB664831
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|13895986|gb|AU182322.1|AU182322
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|29668596|gb|CB664871.1|CB664871
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|29640330|gb|CB645339.1|CB645339
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
EST: gi|29686796|gb|CB683071.1|CB683071
EST:     TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATG                         CTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA
genomic: TGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTA

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: 35 (upstream exon), 74 (downstream exon)
Score: 5

CAAGTGCTTGCGTCTCGGGGCAGCCGAGTACCTGGTCAAGCCACTGCGCATGAACGAGCTGCTGAACCTCTGGACCCATGTGTGGCGGCGAAGGCGGATGgtaaagggga ... gtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcgttgctgtagcgtgtatgagttgatcttaagttgaatgttggtgttggcagCTTGGTTTGTCGGAGAAAAACTTCTTCAATGACAATTTCGAGTTGGCGTTATCGGAACCTAGTGACGCCAATACCAACAGCACCACTCTTCTCTCGGATG
                      agttgat  putative branch site (score: 5)
                           atcttaa  TA-rich tract