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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttttggatttctacctacatgcaatgccaaatcttttttccctagtgttttcattttagtaaatcaattttgtaaacattctaaataaataaatgataaaagttgaaaaagatgctctggaggactgaccattatgaggaaactgttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT

Basic information

species Oryza sativa
transcript LOC_Os10g42100.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G033526_T01 (Zea mays), 3'ss of exon 10
gtaagttttttttggatttctacctacatgcaatgccaaatcttttttccc-tagtgttttcattttag----taaatcaattttgtaaacattctaaataaata-aatgataaaagttgaaaaagatgctctggag--gactgaccattatgaggaaactgttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT
|| ||||  |||  | || |     |     |   || |||||||  |    || | | |       |     |  ||| |  | ||  | |  ||   | |||  ||||||  || |||  |||  ||||||||||  ||||||   |||   || |||  |||||| |||||||||||||||||||| || |||||||||||||| ||  | || ||| ||||| |||| ||||| || ||||| ||||||||||| ||||||||||| 
gtgagttcctttgtggttccccttcatgacaataacctaatctttcatgtgatattatctatgaaacatgctttgcatcgagctagttcatagccttcctgaatccaatgattgaaattggcaaatgtgctctggagtagactgatattta--ggggaacaattgttgtagGGAACGAGTGAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC

upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 10
gtaagttttttttggatttctacctacatgcaatgccaaatcttttttccctagtgttttcattttagtaaatcaattttgtaaacattctaaataaataaatgataaaagttgaaaaagatgctctggaggac---tgaccattatgagga---aact---gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT
|| ||||  |||  | || |     ||   ||||  ||         ||  ||  |   |   || ||   |||| ||   ||  | |  | |||    | |||||  || | |  ||| ||| |||| || ||   ||||  ||| | | |   ||||   |||||||||||||||||||||||| ||| || |||||||||||||| ||  | || ||| ||||| |||| ||||| || ||||| ||||||||||| ||||||||||| 
gtgagttcctttgtggttccccttcacg-acaataaca------ccatctttaacgcgat--attgagatcatcagttc-atagccttcatgaat---cagatgatctaaataggcaaatatggtctgaagtacacttgacatttaggggaactgaactatcgttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC
















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|58676860|gb|CK065547.1|CK065547
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|29661411|gb|CB657686.1|CB657686
EST:     CTTTTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|29614922|gb|CB619935.1|CB619935
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|58691037|gb|CK079724.1|CK079724
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|58660571|gb|CK049251.1|CK049251
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACCATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|58677681|gb|CK066368.1|CK066368
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|88520722|gb|CI446378.1|CI446378
EST:     TCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGCCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: TCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|88333381|gb|CI642418.1|CI642418
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCC
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCC
EST: gi|88272849|gb|CI386109.1|CI386109
EST:     CCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|58666184|gb|CK054870.1|CK054870
EST:     CAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|22307162|gb|BQ908384.1|BQ908384
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTAC-ATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|88489512|gb|CI426784.1|CI426784
EST:     CCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|86519992|gb|CI160198.1|CI160198
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|218497937|gb|FG958969.1|FG958969
EST:     CTTTTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTTTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|29628928|gb|CB633939.1|CB633939
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|88478930|gb|CI416201.1|CI416201
EST:     GCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: GCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
EST: gi|88835790|gb|CI370895.1|CI370895
EST:     CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGA                         GGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA
genomic: CTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTA

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), 74 (downstream exon)
Score: 42

CCCTTTGCACCCCAATTATTGTGTTTACACGAACCGGCTCCATGGCAGTCCTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttt ... gttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgaaaaagatgctctggaggactgaccattatgaggaaactgttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT
                       gactgac  putative branch site (score: 42)
      aaaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttttttggatttctacctacatgcaatgccaaatcttttttccctagtgttttcattttagtaaatcaattttgtaaacattctaaataaataaatgataaaagttgaaaaagatgctctggaggactgaccattatgaggaaactgttgttgcagGGAACGAGTGAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA