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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 9
gttagtatgctattgttgtt-ttgttctgtgg--atactaataact-ctcctacctgcttgtg-gttgtgtg---gatggcctagcttgttgggccgaatcataggtccag----------tccttcaagtttcctcagttttggtcaatt-tacagtcataa----cctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
||| ||||| |  || ||    |   |  |     || |  |  || || |||  ||  | || |     ||   ||| |  |  |   || |    |   | ||    ||          | |||    | | |||  |||||| ||||  || ||| |||     ||||||| |    ||||||||||||||| |||||||||||||  |||| || ||  | ||||||||||| ||||||||||||| |||||||||||||||  |||| ||  |||||||||
gtttgtatgtttctgatggcactagccaataatcgtagttttggctactactagttgagtatgtgcgacatgacagattgtgttccacattagttaaagaaaaagacatagaagatgtttttgcttttcctctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 9
gttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
|||  | | |   | ||  || || |||  |||    || | |   |    ||||| | |            | ||   | || | | ||| |  |  |    |  ||||  ||   |  |||||| |    ||   |||| |   | ||||| |  ||||||||||||||| |||||||||| || || || ||||| || || || |||||||||||||| |||| ||| |||||||||||  | ||||| ||||||||||
gtttat-tacccatattccttagtcctgacgatgtcgatcatttatca---tgcttttagc----------acgtaatgtatttgactgaagccaattttttttatttca--ttgtgtgtgttttgtttttgtttttgtca-atggtgtggtgatacctgcagGTTGCAAGGATTCTAATGAAAACCGTTTCTCAGTTGGCATCCGGGAAACAGCCTGTTGGCACAATGGCCTACATGGGCAAAGTGCAGTATTTGATGCAAT

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 7
gttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
                                                         |  ||||  || | || | ||          ||    |  | || | | ||     ||| |||    | ||    | ||| || ||        |   |  |  ||||||| |||||||| ||||||||||| || ||| | |  |||||||||||||||||||| || || ||||| |||||     |   | | ||||||||||
--------------------------------------------------------ctcattgttgggcttgctttgcccaactactagagatgttagccctggcatta----ttcttcaaa--tagtgtgctaacattc-tactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT

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|86906713|gb|CI291165.1|CI291165
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|29681783|gb|CB678058.1|CB678058
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAG
EST: gi|58670583|gb|CK059269.1|CK059269
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|218498819|gb|FG964003.1|FG964003
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|29641670|gb|CB646677.1|CB646677
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58693078|gb|CK081765.1|CK081765
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58652726|gb|CK041406.1|CK041406
EST:     AGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: AGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58598568|gb|CK009096.1|CK009096
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|87023655|gb|CI286406.1|CI286406
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGCTTTCTAATAGAAGACTGTATCCCAGTTAGCTTCTGGAAAAC
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGG-TTTCTAAT-GAAGACTGTATCCCAGTTAGCTTCTGGAAAAC

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: 75 (upstream exon), 72 (downstream exon)
Score: 62

TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
                              tcataac  putative branch site (score: 62)
                                           tgctctct  putative PPT
                   tcaattta  TA-rich tract