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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG

Basic information

species Oryza sativa
transcript LOC_Os03g58240.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G305254_T07 (Zea mays), 3'ss of exon 4
gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
|| ||||   ||||| | | |          |||| |||||||||||||    | || |  | ||     | || | ||  |||      |||||||   || ||||||||||||||||| |||||||| || || || || |||||||||||||||||||||
gtttgtgccgagaaacgaactc--------attccgatttactttttct----tggagaattaac-----tattagaatgttttc-----tttcttt---ggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019361_T01 (Zea mays), 3'ss of exon 5
gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
|| ||||   ||||| |   |          |||  |||||||||||||| ||| || |  | ||           ||| |   | |||  |  || | ||| |||||||||||||||||||||||| | ||||| ||||| |||||||||||||||||||||
gtttgtggctagaaaagagctc--------attctgatttactttttctaggatggataattaac-----------tattagaatgttc--tctttctttggtagGATATTTGCTTTGGCAACTGTCCTAAGTTCGGTGCTTATCTACAACCTTCCTGAGACG

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 5
gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgtt-ggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
                  | ||     |  |    ||||    | |||| || |  |     || ||  |||||  ||    ||||  |  | | |  | | |||||||||||||||||||||||||||||||||| ||||| || || ||  | || ||||||
---------------gtaattgctttcagatcatgcattc-tgtgttctgtgttgaatca--tatatgattgtttagttggctttttcttgtgtttgcttttgcagGATATTTGCTTTGGCAACTGTCTTGAGTTCCGTGCTCATATATAATTTGCCCGAGACG

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G16130.1 (Glycine max), 3'ss of exon 4
gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
                  | ||     |  |    ||||    | |||| || |  |     ||   |  | | | || | |||| ||  | | |  | | |||||||||||||||||||||||||||||||||| ||||| || || ||  | || ||||||
---------------gtaattgctttcagatcatgcattc-tgtgttctgtgttgaatcatatatgattgtttagttagctttttgtt-gtgtttgcttttgcagGATATTTGCTTTGGCAACTGTCTTGAGTTCTGTGCTCATATATAATTTGCCCGAGACG

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|29636549|gb|CB641558.1|CB641558
EST:     GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAG                         GATATTTGCTTTGGCAACTGTCTTGAGTTCAGAGCTAATCTACAACCTTCC
genomic: GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
EST: gi|29629845|gb|CB634854.1|CB634854
EST:     GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAG                         GATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
genomic: GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
EST: gi|40487583|gb|BX898537.1|BX898537
EST:     GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAG                         GATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
genomic: GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
EST: gi|29666666|gb|CB662941.1|CB662941
EST:     GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAG                         GATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
genomic: GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
EST: gi|29629844|gb|CB634853.1|CB634853
EST:     GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAG                         GATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC
genomic: GATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCC

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: 38 (upstream exon), 61 (downstream exon)
Score: 8

CACCTGTTGAAATGGACATTGATGGTTCAAAAGTGTCTGTCCTTTACCTTGATACTGAAGGATTTGAGAGTGTTGGGAAGTCAAATGTATATGATGATAGgtctgtgtgc ... tttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
                               ttttattcatttcttt  CT-rich tract
                          tatcattttattcatt  TA-rich tract