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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

Basic information

species Oryza sativa
transcript LOC_Os06g12220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G177237_T01 (Zea mays), 3'ss of exon 2
---gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
   || | ||  ||  | |  | ||    | | |||    |   | | | |||  | |  ||| || || | ||   || ||   |||| |||  | ||||||||||| ||||| ||||| ||||| ||||||  |||||| ||||||||||| |||||||||||||||||| ||||||| ||| |||||||||||||||| 
catgtgactaaaatgatttgttgatgttgt-tgttgatgatgacactatgtgagcactattgtcat-atttctaatcattttctgttttggcaactttgcagATATGCTTCTGTTAGAGCGATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
---gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
   || | ||  ||  | || | ||    | | |||    |   | | | |||  | |  |||||| || | ||   || ||   |||| |||  | ||||||||||| ||||| ||||||||||| ||||||  |||||| ||||||||||| |||||||||||||||||| ||||||| ||| |||||||||||||||| 
cttgtgactaaaataattttttgatgttgt-tgttgatgatgatactatgtgagcactattgttat-atttctaatcattttctgttttggcaactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
gtaagtattat-tttgttgtaattcaatattttgccattttgattgtttgattatttc--------tgttattatatatatatatatttact--tttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
|||||||| |  |||||||| | |  | | | ||    |||  |  | |   || ||         | || |||||| | ||   | || ||  ||| |||| | ||||||||||| ||||| ||||| ||||| ||||||  |||||| ||||||||||| |||||||||||||||||| |||||||||||||||||||||||||||| 
gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
--gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatata-tatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
   |   | |||||||| ||    |   ||| |    |  |  |||||| ||  ||   |    | ||  ||  | | |  || ||||    | | || |||||||||||| || || ||||| || |  || |||||||||||||| ||||||||||||||||| ||||| || ||||| || |||||  | ||||| |||
tgtttgtttttattttgctggttcttgttatgtgttaagct--attgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatat-atatatttac-ttttcgcactt--ctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
                                                  |    | | ||   |    ||| | |   ||| | | |     ||   ||||||     |  | ||| | | ||  || |   ||||||   |   |||||||||||| ||  | || || || || |  || |||||  ||||||||||||| ||||||||||||||||| || ||||| || |||||  | ||||| |||
gtaagtgcaatcttaatcttcctcgtttccttacatacactatgtgtttttgttgaatgttccatctgcatttattccattgtcctgtgagaggtcaaattattgtgactgatttattttttattgatgtgggttttcgtgttgtgctgcagATATGCTTCAATTAGGGCGATTGAGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTT

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G01160.1 (Glycine max), 3'ss of exon 2
------------------------------------gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
                                    | |     | |||||||| |  |   | ||       ||  |||||| || |  |||   ||||||  || |   | ||    ||| ||     | ||||||||| ||  | || ||||| || |  || |||||| ||||||||||||| ||||||||||||||||| || ||||| || |||||  | ||||| |||
gtaagcaaaatcttgatcttcctcttttccttacacgcacaatgtgttttgttgaatgttccttttgcatttattccattgttggactcattca--tattattgatgtgggttttcgtgttttgc-----ttcagATATGCTTCAATTAGGGCAATTGAGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G20570.2 (Glycine max), 3'ss of exon 1
gtaagtattattttgttgtaattcaatattttgccat--tttgattgtttgattatttctgttattatatata-tatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
 | | | || |||  || || ||   |   | |  ||  ||| |    ||| ||     |    | ||  ||  | |||  || ||||   || | |  |||||||||||| || || ||||| || |  || |||||||||||||| ||||||||||||||||| ||||| || || || || |||||  | ||||| |||
-ttaat-ttgtttgtttttattttgctggctcgttatgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G11770.1 (Glycine max), 3'ss of exon 2
gtaagtattattttgttgtaattcaatattttgccattttgattgtt-tgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
|||||||||   ||    |  || ||| |       ||   | | || || | |    |||    || | ||| |    ||    |  |    |   ||||||||| ||  | |  || ||||| || |  |||     |||||||||||||||||||||||| ||||| || ||||| || |||||  | |||||||| 
gtaagtattgcctttagttttttgaatgtaaaatgtttactacttttgtgctaaaaagtgtagcaatgtgtatctgaggttttggtatgtgagtg-acagATATGCTTCAATCAAGGCCATAGAGACTAGGTCTAGGACTGATGATCAGCAATGGCTCACTTATTGGGTTCTCTACTCTTTGATCACACTCTTTGAGCTC

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
---gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
   ||| ||  |||  | | ||  ||  | || ||    ||||  || | |||       |    | | |  | | | |   |    |     |||   ||||||||||||  | || ||||| || || || || |||||||||||||||||||||||||| ||||||||  |||| ||  | |||||  | || ||||| 
catgtatgttctataatat-gtggtttga-atgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|33662703|gb|CF293670.1|CF293670
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|33682572|gb|CF310811.1|CF310811
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|58600408|gb|CK010936.1|CK010936
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|58681131|gb|CK069818.1|CK069818
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|58690333|gb|CK079020.1|CK079020
EST:     GGCATTAGTTTCACNTTGCTTATCCATT                         ATAGTGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGC
genomic: GCCATTAGTTTCAC-TTGCTTATCCATTgtaagtatta ... acttctgcagATA-TGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGC
EST: gi|88367310|gb|CI566276.1|CI566276
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|88760470|gb|CI770026.1|CI770026
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|117221019|gb|CT852619.1|CT852619
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|88745841|gb|CI769201.1|CI769201
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|3766943|gb|AU031053.1|AU031053
EST:     GCCATTAGTTTCANTTGCTTATCCATT                         ATATGCCTCTGTGAGAGNAATAGAAAACAAAATCTCCTGTTGATG-TCAGC
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAA-CAAAATCTCCTGTTGATGATCAGC
EST: gi|88431065|gb|CI574236.1|CI574236
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|2312240|gb|C28395.1|C28395
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|218478179|gb|FG968243.1|FG968243
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|86906935|gb|CI291277.1|CI291277
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
EST: gi|426583|gb|D22408.1|D22408
EST:     GCCATTAGTTTCACTTGCTTATCCATT                         ATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA
genomic: GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCA

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: 74 (upstream exon), 70 (downstream exon)
Score: 32

GCCATTAGTTTCACTTGCTTATCCATTgtaagtatta ... acttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
 gtttgat  putative branch site (score: 32)
                                     cttttcgcacttct  putative PPT
     attatttctgttatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT