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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacgtgagatctctttttttaactatatatttttattgaagaacaaaaaattgacaccaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA

Basic information

species Glycine max
transcript GLYMA13G42990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
------------gtgagacgtgagatctctttttttaactatatattttta--ttgaagaacaaaaaattgacaccaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
            |    ||    |||    || ||  ||    ||||  |    |  |    |  || |||  |        |  ||| | | ||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| || || ||||| |||||| | |||||||||||||| || ||
gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattattt-gcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
--------------------------------------------gtga-gacgtgagatctctttttttaactatatatttttattgaagaacaaaaaattg--acaccaataaaaaaattgtc-tcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
                                            |||      |||  |     ||||||  | ||| |   |||      |   ||  |||  | | ||       | || |  | |||||||| || |||||||||||||| || ||||| |||||||| || ||||| |||||||| || || || || |||||  | ||||| |||||||| |||||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gtgagacg-----tgagatctctttttttaactatatatttttattgaag--aacaaaaaattgacaccaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
|| || ||     |    |||  ||||   |    |   |||  ||||    |    || |    | |  ||   |   || | | |||||||||||||||||||| ||||| || || || ||||||||||| ||||| || ||||| ||  | || || ||||  || ||||| || ||||| |||||
gtcagtcgcctcttttattctacttttagcatcccaagctttgcttgatttcactgtaacaaaatctcagatcttatgcttctattgcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
gtgagacgtgagatctctttttttaactat--atatttttattgaagaacaaaaaattgacaccaataaaaaaattgtctcg-------cagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
||      |   | ||||| ||||  ||||  ||||  || |   | |     | ||||    |  | | || |||   |||       ||||||||||||||||| |||||||||| ||||| |||||||| || ||||| ||||| || || || ||||| |||||| |||||||||||||||| || ||
gtagccatttgtaactcttatttttgctattgatatagttgtaacacatttctagattggt--ctgtgacaatattccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtga--gacgtgagatctctttttttaac----tatatatttttattgaagaacaaaaaattgacaccaataaaaaaattgtctc--------gcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
|| |  | | |    | |  ||  | |||    | |   ||| || |  | | ||    |  ||  |  || ||     || |          | |||||| || ||||||||||||||||| ||||| |||||||| || ||||| || |||||||| || || || |||||  | |||||||||||||| |||||
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------gtgagacgtgagatctctttttttaactatatatttttattgaagaacaaaaaattgac-accaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
                 |   | ||| | | |  || ||      | || |    |  |||| |    ||   || | || |     |   || | |||||||| || |||||||| || ||| | || |||| ||||||||||||||| ||||||||| |  | || || |||||  |||||||||| ||||| || | 
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT

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|207797777|gb|GD770819.1|GD770819
EST:     GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAG                         ATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
genomic: GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAGgtgagacgtg ... tgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
EST: gi|51342082|gb|CO983347.1|CO983347
EST:     GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAG                         ATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT
genomic: GATCACTTTGAAAAACGTCAAAAAATGGCTATAAATCTGAAGTACATAGgtgagacgtg ... tgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatttttattgaagaacaaaaaattgacaccaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA
                        aattgac  putative branch site (score: 3)
                                            ttgtctc  putative PPT
     tttttattgaagaaca  TA-rich tract