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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttacgaccaaaccacctgaactttctttcgatgagacaaaactagctagtaatatgtcaaatattcagattttttttataatgcgtttgagcttaccatgtcctgatccatttctatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG

Basic information

species Oryza sativa
transcript LOC_Os10g04860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 3
gtacttacgaccaaaccacctgaactttctttcg-atgagacaaaactagctagtaatatgtcaaatattcagattttttttataatgcgtttgagcttaccatgtcctgatccatttcta--tcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG
                    | |  ||||||| |  | |    ||| ||   || ||||    ||||||       |||| |||||   |    ||||||||||||| || | | |||  |  ||| ||||||||| |||||||||| ||| ||  ||||||| |||| |||||||||  |||| ||||  || |||||||| |||||||||||||| ||| ||||||| |
-------------------gtaatgtttctttagtgtcatttcaaattacacagaaatag---aaatatg------ttttgtataaccaggc--agcttaccatgtcttgttgctttttcaattcactcagATTGCTGAAACACAAAGATATGCTAATATGGCTGCAAAGCAAGCTGTTGTTGAGTATAGCACAGAAAATCTGCAGCCACCAATTCTGACAATAGAAGATG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G899851_T01 (Zea mays), 3'ss of exon 3
gtacttacgaccaaaccacctgaactttctttcgatgagacaaaactagctagtaatatgtcaaatattcagattttttttataatgcgtttgagcttaccatgtcctgatc-catttctatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG
                                  |||   |  || |  |   | | || ||| | |       ||   ||    |   |   | ||| |   ||| || |    ||||||||| |||||||||  ||||||| || || ||||| ||||| |||| |||||| || ||||| ||||  || |||||||| |||||||||||||| ||| ||||||| |
-------------------------------gtaatgtttcctaagttccctttcacatttcacaaaactgttcttaagtttatgtctatccaaccttgctgcgtcatgttggtttttctatcactcagATTGCTCAAACACAGAAGTATGCCTACATGGCGGCAAAGCAAGCCGTCATTGAGTATAGCACAGAAAATCTGCAGCCACCAATTCTGACAATAGAAGATG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G019799_T01 (Zea mays), 3'ss of exon 3
gtacttacgaccaaaccacctgaactttctttcgatgagacaaaactagctagtaatatgtcaa-atattcagattttttttataatgcgtttgagcttaccatgtcctgatccatttctatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG
            |     | | ||||  | ||  || |||  |||  ||| ||||||| ||||   ||| |  |   | || | ||| |  |  ||||||||| | | || |   |||| ||||  |||||| | ||||||||||  || || |||||||| |||| |||||||||  |||| ||||  || |||||| | |||||||||||||| ||  || |||| |
---------gtaaggttgcttaaactgaccttt-ataagattaaatgagccagtaataagtcagtgtatacccagaatcttgaaaattctatcaagcttaccacgccatgttggttttcgatcacacagATTTCTGAAACACAAAGGTATGCTTATATGGCTGCAAAGCAAGCTGTTGTTGAGTATAGCACAGAAAATTTGCAGCCACCAATTCTGACTATACAAGATG

upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 3
gtacttacgaccaaaccacctgaactttctttcgatgagacaaaactagctagtaatatgtcaaatattcagattttttttataatgcgtttgagcttaccatgtcctgatccatttctatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG
            | |       |   | ||||||||   ||||||| |  ||             | || |  | | |   ||| |    |||    |  |||||  ||||   |||||||   ||||||||| |||||||| || || ||||| ||||| |||| ||||||  | ||||| ||||  || |||||||| |||||||||||||| ||  ||||||| |
---------gtaatatttttcaagtgtcctttcgatttcacaaaaccatttatc-----------tgtttatgtctatccaatatta---ttg----tgtcatgt--tgatt--tttctattgctcagATTGCTGAAACACAGAAGTATGCCTACATGGCTGCAAAGCAAGCCATTATTGAGTATAGCACAGAAAATCTGCAGCCACCAATTCTGACGATAGAAGATG

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), 67 (downstream exon)
Score: 11

CGGTGGAGAAAATGTTGGATCCTGCTTCCCAATGTTAGGAGATGAAGCACTTTTTGCTGATCCAGTTGCTGAATTCGCTGGTCAAAATATCGGCGTTGTGgtacttacga ... tatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttataatgcgtttgagcttaccatgtcctgatccatttctatcattcagATTGCGGAAACACAAAAATACGCCTATATGGCAGCAAGGCAAGCTGTGATTGAATATAATACTGAAAATCTTCAGCCACCAATTCTAACAGTAGAAGACG
                               tcctgat  putative branch site (score: 11)
                                     tccatttct  CT-rich tract
     tttataat  TA-rich tract