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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatctacttgatctttgaaccatttctgtttgagattttctgtataattattatatattttcttctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTTATGTGTGCCTATGGAAAATACCAG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 15
--------------------------------------gttatctacttgatctttga-accatttctgtttgagattttctgtat---aattattatatattt-tcttctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTTATGTGTGCCTATGGAAAATACCAG
                                      |  |  | | | |   ||   |  ||   ||   |  | |||    ||   |||   || |||||  | |||| ||||||||| ||| ||||||| |||||||| ||||||| | | |||||||||||||| ||||||||||||||||||||||||
gttaatgacatatatagtatgctttgttttttccccctgggaattgcataagaattagtattatgcatgcaagtaagtttgcagattctaatctgtacatattggttttctattttcagGAAGCTTCTGAAGAATTAGTACCCCACTTGGAAGTAATTTTGCAGCACCTCATGTGTGCCTATGGAAAATACCAG

upper sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 15
------gttatc-tacttgatctttgaaccatttctgtttgagattttctgtataattattatatattttct--tctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTTATGTGTGCCTATGGAAAATACCAG
      |||||  | |    |  ||    ||||||||| |     | | | | ||  |   |   ||| | |  | |    |||||||||||| ||| |||||| ||||||||||| ||||||| | || ||||| |||||||| | ||| || ||||||
gtttctgttattatgcagtgtaattattacatttctgtctttagatatatctctagatcccaatgattgtttgatttaccatcagGAGGCTGCAGAAAAGTTAGCACCACACTTGGAAATTATTCTACAACACCTAATGTGTGCTTTTGGGAAGTACCAG
















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|33678128|gb|CF306367.1|CF306367
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58668781|gb|CK057467.1|CK057467
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGACTTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58660018|gb|CK048698.1|CK048698
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTGGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58662883|gb|CK051569.1|CK051569
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGA
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGA
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58608786|gb|CK036819.1|CK036819
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         G---CTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT

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: 43 (upstream exon), 70 (downstream exon)
Score: 6

ACAATTTGATAAAATCCTCTTAGGTTTATTAAGGAGGGTTTTGGATACTAACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTTATGTGTGCCTATGGAAAATACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttctgtttgagattttctgtataattattatatattttcttctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTTATGTGTGCCTATGGAAAATACCAG
                                    tattttcttctgtttt  CT-rich tract
               attttctgtataatta  TA-rich tract