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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgcttctaccattgcttatgttcaacaagttgtgctctccagttattaatcttatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA

Basic information

species Glycine max
transcript GLYMA18G48050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g41950.1 (Oryza sativa), 3'ss of exon 5
gttggtgcttctaccattgcttatgttcaacaagttg-tgctctccagttattaatcttatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
                                 |||| || |        ||  | ||||     | |  ||  | | |   ||     ||   | |   || |     || ||| ||     || |||||||||||||||||||||||||| |||   || | ||| || ||    ||  ||   | |||||| || || | ||| || ||
---------------------------------gttgatgtttcttgaacatctagctta-gccctagcccttggttttcacatctttctgatcagtccttttttgcc-tgcagAGCA-----CGGTTGGTAAATATGTGTAAATATATGGGGATCCAACCTTTTGGTACAGACCACTACCTGACATTCATGCTTCGGAAGAAATTGCAAGA

upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145905_T01 (Zea mays), 3'ss of exon 5
gttggtgcttctaccattgcttatgttcaacaagttgtgctctccagttattaatct-tatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
                                 |||  ||  |||  |  |  || | || |||    | | |   ||   || | || |    | ||||||   |  ||   |  ||| || ||||||||||||||||| ||||||||||| ||| | || | ||| || |||   ||  || | | |||||| ||||||| | | |||||
---------------------------------gttaggcattcctttagtatatgtatacattcatagtcacaattacactagtgac-taaacagttggttggcactatcctg--cagACCACGCTTGGTAAATATGTGCAAATATATGGGTATCCGGCCTTTTGGTACAGATCACTACATGAGGTTCATGCTTCGCAAAAAACTTCAGGA

upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G314656_T01 (Zea mays), 3'ss of exon 5
gttggtgcttctaccattgcttatgttcaacaagttgtgctctccagttattaatcttatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
        ||| ||  |  ||| | |   ||    ||||        | || || ||   ||      | | |  || || | |||  ||  |  |||||| ||    || ||| ||     ||||||||||||||||| ||||||||||| ||| | || | ||| || |||   || ||| | | |||||| ||||||| | | || ||
-------gttcgacggtc-cttttatcttac---ctgtgtaaattgatcatcaaactatcat-----agttacaatagtg-actaaactgt-tgcttggttttgtttctgcagATCA-----CGCTTGGTAAATATGTGCAAATATATGGGTATCCGGCCTTTTGGTACAGATCACTACTTGAGGTTCATGCTTCGCAAAAAACTGCAAGA

upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G65540.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggtgcttctaccattgcttatgttcaacaagttgtgctctccagttattaatcttatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
                       |  | ||| |||      ||  |  ||||  |  |    | |   ||| |  | |||  ||    ||   || |  |  |    || |    |||| | || |||||||||||||| ||||| ||||| || |||||||  ||||||||||||||||| ||||| ||||| || ||||||||||||||
----------------------gttatgaactagtcaaaa-ctgtatctattggtaatgcgatatt--gcttctgtcttggtttgttttgttaatcttatcttccttattg----cagGTCCCGATTGGTAAATATGTGCAAATACATGGGTATTAGCCCATTCGGAACTGATGCATATTTACGTTATATGCTTCGGAAAAGATTACAGGA

upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0220g00090.t01 (Vitis vinifera), 3'ss of exon 2
gttggtgcttctaccattgcttatgttcaacaagttgtgctctccagttattaatcttatattttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
        |  |    || ||  | |||  | |       | |  |  ||||  | || | |||| |   ||   | ||| |  ||  | |||| |||| |    ||||     |||||||||| |||||||||||||| || |||||||| ||||||||||||||||||||||| ||||| ||||| ||||| || |||||| | ||   
--------tcttcttcttcctcctcttccccca----caatatatatatatttttttt-tctttttgttttctctttttgaaaaaaactacctacttgggttgttaaat-----acagGCCTCGGTTGGTAAATATGTGCAAGTATATGGGTATCAGCCCATATGGAACTGATGCGTATTTACGTTATATGCTTCGGAAAAGACTTCAATG

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|14205472|gb|BG839150.1|BG839150
EST:     GGATTTGCCAAATTATTTAATGATGAGCTCACCCTGGATAACATTAGCAG                         GCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAAC
genomic: GGATTTGCCAAATTATTTAATGATGAGCTCACCCTGGATAACATTAGCAGgttggtgctt ... tggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggctccgctattgtattaacatgcctatttggttatgaaaatggagaacagGCCTCGCTTGGTAAATATGTGTAAATATATGGGCATCAGCCCATATGGAACTGATGCATATTTGCGTTACATGCTCCGCAAAAGATTACAGGA
                 tattaac  putative branch site (score: 1)
            tattgtattaacat  TA-rich tract