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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttttagccatggattaccctctggttgggtattcaatatttgagttttcacactttgatccttgtatttctagGTCATGATGCGTCTATTCAGTCCCCGGAAAACGACATTGCTTTTTGTTATACGTGATAAAACAAAG

Basic information

species Glycine max
transcript GLYMA09G02490.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 5
gtagtttttagccatg--gattaccctctggttgggtattcaatatttgag----ttttcacactttgatccttgtatttctagGTCATGATGCGTCTATTCAGTCCCCGGAAAACGACATTGCTTTTTGTTATACGTGATAAAACAAAG
||| || |  |   |      || ||| ||     | | |  ||  ||||     || | ||| || ||    ||  ||| ||||||||||||||| | ||||||||||| || || ||| |  | |||||||||||||||||||| | |
gtatttatctgttttttcagataacctttgccacagcaatacattcttgatgcatttgtaacatttggacaactgggtttgtagGTCATGATGCGTTTGTTCAGTCCCCGAAAGACAACACTATTATTTGTTATACGTGATAAAACCAGG

upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G390374_T01 (Zea mays), 3'ss of exon 5
----------------------------gtagtttttagccatggattaccc-tctggt--tgggtattcaatatttgagttttcacactttgatccttgtatttctagGTCATGATGCGTCTATTCAGTCCCCGGAAAACGACATTGCTTTTTGTTATACGTGATAAAACAAAG
                             ||  || |   |||    ||  | | | ||  ||   ||   || | |      | |||||| ||    ||  | | ||||||||||||||| | || ||||| ||||| || ||| | || |||||||||||||||||||| | |
gtaccgaggttaaatctgtctttcagggataccttatgcacatatgatatacatatagtcctgatcatctgatgtatag----taacacttggacatctgagtatgtagGTCATGATGCGTTTGTTTAGTCCTCGGAAGACAACACTACTATTTGTTATACGTGATAAAACCAGG

upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 4
gtagtttttagccatggattaccctctggttgggtattcaatatttgagttttcacactttgatccttgtatttct-----agGTCATGATGCGTCTATTCAGTCCCCGGAAAACGACATTGCTTTTTGTTATACGTGATAAAACAAAG
||| |   || ||||   ||    ||| ||    ||||  |||    |  ||  | |   |||  |  || | |||     |||||||||||||  |||| || || || ||||||||| | || ||||||||||||||||||||||||
gtactccctatccatatttttgtatctagtacaatattgcataac--aaattcaataagatgagtcccgtttctcttctatagGTCATGATGCGCTTATTTAGCCCACGCAAAACGACACTACTGTTTGTTATACGTGATAAAACAAAG

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|17023193|gb|BM094227.1|BM094227
EST:     TTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG                         GTCATGATGCGT
genomic: TTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAGgtagttttta ... gtatttctagGTCATGATGCGT
EST: gi|209698106|gb|BW661049.1|BW661049
EST:     TTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG                         GTCATGATGCGTCTATTCAGT
genomic: TTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAGgtagttttta ... gtatttctagGTCATGATGCGTCTATTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctggttgggtattcaatatttgagttttcacactttgatccttgtatttctagGTCATGATGCGTCTATTCAGTCCCCGGAAAACGACATTGCTTTTTGTTATACGTGATAAAACAAAG
                                  ctttgat  putative branch site (score: 5)
                                        tccttgt  CT-rich tract
           tattcaatatttga  TA-rich tract