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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctaatattttctttaaaccttttttcttttatattttgattgtgtcttagatctgtggctcagtatcattgctttctgatgattcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT

Basic information

species Glycine max
transcript GLYMA20G30100.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 8
----------------gttctaatattttctttaaacctttt--ttcttttatattttgattgtgtct-tagatctgtggctcagtatcattgctttc----------tgatgattcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
                 ||||  ||   |  |  |    |||  |   |||||   |   || | ||    | | |     |||   |   | || ||          | |  || |||||||||||||||||||||||||| || ||||| || || ||||||||  | |||||||| ||||| || ||||||||  | ||||| || |||   || |
gtaatgaaaatcctacattcttctacacttctctagttatttgatgaatttatgcctatcttctctccgctGTTATAAAAATCAACCTTGCTTCTCTCACACATGTAATAACTATGCAGGTTATAAAAAATTCTAATGGATGTAATCTTGCTGTTGACATATGGAGCTTAGGATGCACGGTTTTAGAGATGGCTACCTCAAAACCACCATGGAGCCAAT

upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
gttctaat-attttctttaaaccttttttcttttatattttgattgtgtcttagatctgtggctcagtatcat-tgctttctgatg---attcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
||   | | |   ||||||   ||| ||  |||| | |||      | |||||   |  |  ||    ||||  | || |   |     |  |||||||||||||| || ||||| |||||||| || || || ||||||||| | |||||||| ||  |||| ||||||||| | ||||| || |||   ||||
gtatcactgaaaatcttta---cttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT

upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 7
-------gttctaatattttctttaaacctt-ttttcttttatattttgat-tgtgtc---ttagatctgtggct--cagtatcattgctttctgatg---attcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
         |  |    || |||||     | |||| |||| || ||  || ||  ||   ||| |  |   | |  ||  ||  |  |  |         || |||||||||||||||||||||||||||||||||| ||| || ||||||||| | || ||||| ||  |||||||||||||  | || || || |||   ||||
gtactgaaatgaagctcttcctttagtttgtatttttttttttaattcaatgtgcatcacattataatttctgttaacaaaatactaaccatgcagcacaaatgcagGTTATAAAAAATTCTAATGGATGCAACCTTGTGGTTGACATATGGAGTTTAGGTTGCACTGTCCTGGAAATGGCTACCTCAAAGCCACCATGGAGCCAGT

upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 8
gttctaatattttctttaaaccttttttctttta-tattttgattgtgtc--ttagatctgtggctcagtatcattgctt----tctgatga---ttcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
       ||||  |   || | |   || || |  || |||  || | |     |||| | |   ||   | | ||||||    | |||  |   | ||||||||||||||| ||| |||||| |||||||| || |||||||||||| | |||||||||||  | || ||||||||  | ||||| || |||   || |
------gtattaccccaaatcttgcattgttctgctactttagttattttggccagatttatatatcctgacctttgcttatgttgtgacaaatatgcagGTTATAAAAAATGCTAGTGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAAT

upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 7
-----gttctaatattttctttaaaccttttttcttttatattttgattgtgtct-tagatctgtggctcagtatcattgctttctgatga---ttcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
     |  | || || ||   |   ||   |   ||   ||||||| ||| || | || |||| || ||   | || |||  || |||  |   | ||||||||||||||| |||  ||||| |||||||| || |||||||||||| | |||||||||||  | || ||||||||  | ||||| || |||   || |
gtattgccccaa-atcttgcattgtcccgctacattagttattttggttgggtttatatatct-tgactttttttc-ttgtgttgtgacaaatatgcagGTTATAAAAAATGCTAGCGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAAT

upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 7
gttctaatattttctttaaacct---tttttcttttatattttgattgtgtcttagatctgtggctcagtatcattgctttctgatgattcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
||   ||| |||| | |   | |    || ||| ||   || |||     | ||     | |  || | |    |       || |   |||||||||||  ||||| ||||| ||||||||||| |||||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||  |||||
gtcagaatgttttttcttgccataaccttatctcttcatttatgacaagcttttgatagtatttcttacttctctgttcagttgttcgctcagGTTATAAGGAATTCAAATGGTTGCAACCTTGCTGTGGATATTTGGAGTCTAGGGTGCACAGTTTTGGAAATGGCCACAACAAAACCACCCTGGAGTCAGT

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|18690804|gb|BM519652.1|BM519652
EST:     AATCGTGCCCATTGTCATTCAAGGGAACACCTTACTGGATGGCTCCTGAG                         GTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTT
genomic: AATCGTGCCCATTGTCATTCAAGGGAACACCTTACTGGATGGCTCCTGAGgttctaatat ... gatgattcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgattgtgtcttagatctgtggctcagtatcattgctttctgatgattcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
                                         ttctgat  putative branch site (score: 3)
                                       ctttctg  CT-rich tract
                               tatcatt  TA-rich tract