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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtctttcatctacatgtttctcaagcatttagcaatctaatgtcatagacttcagatgcataatcctatttcttgttttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT

Basic information

species Oryza sativa
transcript LOC_Os03g42110.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G378931_T01 (Zea mays), 3'ss of exon 2
gtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | |||| ||||||| |   | | ||     | | |||||||| ||||||||||||||||||||||||||||||| ||||||||| | || || ||||||||||||||||| ||||| ||||| |  ||||||||||| || ||||| |
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G477770_T01 (Zea mays), 3'ss of exon 2
gtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | |||| ||||||| |   | | ||     | | |||||||| ||||||||||||||||||||||||||||||| ||||||||| | || || ||||||||||||||||| ||||| ||||| |  ||||| ||||| || ||||| |
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTACAATACCAGCCCCTGT

upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G535396_T01 (Zea mays), 3'ss of exon 1
gtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | |||| ||||||| |   | | ||     | | |||||||| ||||||||||||||||||| ||||||||||| | ||||||| | || || ||||||||||||||||| ||||| ||||| |  ||||||||||| || ||||| |
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacatacttaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTCAAGGGAGCATCTGATCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
gtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | | || ||||||| |   | | ||     | | |||||||| ||||||||||||||||||||||||||||||| ||||||||| | || || ||||||||||||||||| ||||| ||||| |  ||||||||||| || ||||| |
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G29630.1 (Glycine max), 3'ss of exon 13
----gtaagtgtctttcatctacatgtttctcaagc---atttagcaatctaatgtcatagacttcagatgcataatcctatttcttgttttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
    || |   | |||  ||  | | | | || |||   | ||    || |||||  ||     |   ||   | |    | |   |   |       ||||||| |||||||| ||||||||||| |||||||| ||| | || ||||||||| || | |||||  | ||||| ||    || || || || |  || || |
gtatgttaagtttttttttcctcctatatatccagctgaaattgtgtatttaatgatattatgatactattgttgacatcactatgttgatgtgttgttgcagATTGATAATCTAGTGAAGGGAGCTTCAGGTCAAGCTTTACAAAACCTTAATTTGTTAATGGGATTTCCAGAAAATTTGGGACTTCATTACCTGCCTCTTT

upper sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
------gtaagtgtctttcatctacatgtttctcaagcatttagcaat-ctaatgtcatagacttcagatgcataatcctatttcttgtt-----ttcaa-----caatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
       ||| | || ||  |   |||||||   ||    ||   | | ||| | | | ||  |    ||  ||  | ||||  || | |      ||||        ||||||| |||||||||||||||||||| || ||||| ||  | ||||| |||||| ||||||||||  |||| ||||| || || || |  || || ||  | |
gtatgtttaaatttcctttgtt--catgttttagaattccttcatatttctagtatgaaaggttattaata-atcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT

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|86598735|gb|CI355352.1|CI355352
EST:     ATCATCATATCTGTT                         ATAGATAATCTTGTGAA-GGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: ATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|109712685|gb|CI105293.1|CI105293
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88259008|gb|CI363301.1|CI363301
EST:     AGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: AGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86886108|gb|CI321144.1|CI321144
EST:     TGAATGTCTTTGAGGACAGAATTCCT-CACGTGCCATCATCATATCTTTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86482790|gb|CI125423.1|CI125423
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88908339|gb|CI090932.1|CI090932
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88846739|gb|CI373507.1|CI373507
EST:     CCATCATCATATCTGTT                         ATAGATAATCTTGTGAA-GGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: CCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|89193633|gb|CI116266.1|CI116266
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGGGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86873228|gb|CI328608.1|CI328608
EST:     GGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: GGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|66912884|gb|CX099732.1|CX099732
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86487376|gb|CI130009.1|CI130009
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88219804|gb|CI219364.1|CI219364
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|29612880|gb|CB617893.1|CB617893
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGACCCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86435982|gb|CI107215.1|CI107215
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86426929|gb|CI072026.1|CI072026
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|89196216|gb|CI397218.1|CI397218
EST:     ACAG-ATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: ACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86433430|gb|CI093773.1|CI093773
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTG                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|89175616|gb|CI042637.1|CI042637
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86526816|gb|CI167022.1|CI167022
EST:     TGAATGTCTTTGAGGACAGGATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|89177368|gb|CI250817.1|CI250817
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88845464|gb|CI084389.1|CI084389
EST:     CTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: CTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86431654|gb|CI085265.1|CI085265
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTN                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|88906616|gb|CI375688.1|CI375688
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTCTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86867318|gb|CI337812.1|CI337812
EST:     TGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
EST: gi|86836098|gb|CI346154.1|CI346154
EST:     TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTT                         ATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT
genomic: TGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAAT

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: 63 (upstream exon), 42 (downstream exon)
Score: 9

TAGCAGCGTTCCTCACACACGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtct ... aacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatgtcatagacttcagatgcataatcctatttcttgttttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT
 atctaat  putative branch site (score: 9)
                               tatttctt  TA-rich tract