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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgttaattgttgaggtactaatctgtacagccaatctgtagtttcatacttacattcaaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA

Basic information

species Oryza sativa
transcript LOC_Os07g07080.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G403493_T01 (Zea mays), 3'ss of exon 15
gtttg-tttgttaattgttgaggtactaatctgtacagc--caatctgtagtttcatacttacatt-caaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
||||| ||| |||  || | ||||  ||||  ||| |||   ||| ||    |||||  || |||  ||   | | | |||||||||| || ||||||||||||||| ||||||||||||| |||||||| |||||||| ||  |||||||   |  |||||||||||| |||||||||||||
gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttg----ttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA

upper sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 8
gtttg-tttgttaattgttgaggtactaatctgtacagc--caatctgtagtttcatacttacatt-caaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
||||| ||| |||  || | ||||  ||||  ||| |||   ||| ||    |||||  || |||  ||   | | | |||||||||| || ||||||||||||||| ||||||||||||| |||||||| |||||||| ||  |||||||  ||  |||||||||||| |||||||||||||
gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttg----ttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA

upper sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
------------------------------gtttgtttgttaattgttgaggtactaatc-tgtacagccaatctgtagtttcatacttacattcaaagtgtttct--acagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
                                 ||||| ||| || |   |  || || | |||  |   ||  |       |    ||   || ||  | ||| |  |||| |||   ||||||| ||||||||| | |||| ||| ||||||||||| ||||||||||||   | ||| ||    ||||||||||  ||||||||||  |
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgattaaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

upper sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 6
------------------------------gtttgtttgttaattgttgaggtactaatctgtacagccaatctgtagtttcatacttacattcaaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
                                 ||| | ||| || |   |  || || |         ||       |  |    ||   || |   | |||  |||| | |   ||||||||||||||||| | |||| ||| ||||||||||| ||||||||||||   | ||| ||    ||||||||||  ||||||||||  |
gttcttattatgctctgaatttttctcttcacatgtattttatttttcccgagacaaaacatgttgattaaaaacacttcccccctttttgtttatttttttttaacagTTGTATGCTATGTGTGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

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: 57 (upstream exon), 73 (downstream exon)
Score: 20

GATCTCAGTGGCTGCTGGAGTGATGCACACCACTGTTTTAACCGCAGATGGTGCTATTTTCTACTGGGTTTCATCGGACCCTGATTTAAGATGCCGACAGgtttgtttgt ... gtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatctgtacagccaatctgtagtttcatacttacattcaaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA
                             tacttac  putative branch site (score: 20)
                                            tgtttct  putative PPT
                        tttcata  TA-rich tract