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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcccctactctaatggttagttccaatttattggttcatttctctgtgtttgataagattttgcctctgctgtgcatttcaatattatatctaaactgtgctgcttatagcttatcaaactactcttgctcataaagatgcaacttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG

Basic information

species Oryza sativa
transcript LOC_Os01g08700.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 6
gtaaggcccctactctaatggttagttccaatttattggttcatttctctgtgtttgataagattttgcctctgctgtgcatttcaat-attatatctaaactgtgctgcttatagcttatcaaactactcttgctcataaagatgcaacttttat-gcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG
                                                        |  | |   ||      |  ||   ||| | |  || | | |     |   |    ||    |||   | |||| |||||||| ||    ||| ||| |   ||| |||||||||| ||||||||||||||||||||||||||||||||||| ||  ||||||||||||| |||||||| ||||||||||| | |||||||| ||
--------------------------------------------------------gtgaggccattagtatcgtggtcagttttagttgttctctttgtgtcgactttgagattcgctattcta-tactgttgctcattaa----caattttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 5
gtaaggcccctactctaatggttagttccaatttattggttcatttctctgtgtttgataagattttgcctctgctgtgcatttcaatattatatctaaactgtgctgcttatagcttatcaaactactcttgctcataaagatgcaacttttat-gcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG
                                                 || |     ||   |||    | | || |   | |   | ||   | | |  | | ||  || ||           |||| || ||||| ||    ||| ||| |   ||| |||||||||| || |||||||||||||||||||||||||||||||||||  ||||||||||||| |||||||| ||||||||||| | |||||| ||||
------------------------------------------------gtgaggccattacagtttcagttgttctctttgtgtttgtgttgactttgagttttacta-ttcta-----------tactgtttctcattaa----caattttcaccacagCAAGAGTACTCAGAACAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTCTTAACTCACTACAATAGGCCAATTTTCAAAGTTGAACGCCAACACAGTG
















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|29667209|gb|CB663484.1|CB663484
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|29642016|gb|CB647023.1|CB647023
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|29636922|gb|CB641931.1|CB641931
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|88369882|gb|CI680559.1|CI680559
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|29646260|gb|CB651267.1|CB651267
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|29636923|gb|CB641932.1|CB641932
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|88587781|gb|CI705554.1|CI705554
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|88361618|gb|CI680183.1|CI680183
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|88369175|gb|CI680281.1|CI680281
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|58590243|gb|CF988551.1|CF988551
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACGCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
EST: gi|88454127|gb|CI694894.1|CI694894
EST:     ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAG                         AAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT
genomic: ATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTT

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: 72 (upstream exon), 75 (downstream exon)
Score: 80

GCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTTCCCGTTCATGTCCTTCATCTCTTTATTTAGCCATACTTCTGAGgtaaggcccc ... ttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgcttatagcttatcaaactactcttgctcataaagatgcaacttttatgcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG
                                            cttttat  CT-rich tract
                                          aacttttat  TA-rich tract