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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG

Basic information

species Glycine max
transcript GLYMA18G03480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 1
gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatc-tcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG
                         |  ||  | | |||       |||   |  |   || || || |  | |  ||      |    || | |  |     |||  ||| || |   |||| |||||||||||||| |||||| ||||||| ||| | ||||| |||||||| || ||||| || |||||||  ||||| ||| |||| 
--------------------gtatgcagtttgtgtgttttacaggttctggcaaataattttagttccttacctgtttaggtgttgtatttgcttaatgaatgttttgtgtatttg-atagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAACCAGACACAGGTTGATAACATTGCTGAGCTGGAAAGAAG-

upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G439457_T02 (Zea mays), 3'ss of exon 2
gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG
           ||      ||   |    ||| | ||||||        |||  || |  |||  |  |   |   | | ||    |  |   | ||| | ||||    | |||    |||| |||||||||||||| || ||||||||||| ||| | |||||||||||||| || || || |||||||||   ||||| ||||| || 
----------cctgatatgcttgatgatctctaagttttctaggaag--tttgctttctctca--ttgcctttttcttaccatacaggct---tatttagtattttgcctattg---tagGTCAGTTTGAGTGCATTTGCATTCTTGTTCTCTGAGTTGGTTCAGTACAACCAGACTCAAGTTGACAACATTACTGAGCTGGAACGGAG-

upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG
                    | |   ||||||| || ||      || | || |   ||||| ||| ||| | |  |  | | |  | ||    |||| | |  ||   |  || || |||| || ||||  ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| ||||| || |  || || ||| |||| 
-----------------gggttttgatcttcttcttctttgatctctttattgtgatcattc-gatttcgagcatctgctgatt--ggttagtcgttttggaactgtacttgtgttgtagGTGAGCTTGACCGCATTTGCTTTCTTATTCTCGGAGCTCGTTCAGTACAATCAAACCCAGGTTGACAATATAGCTGAACTTGAAAGAAG-

upper sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG
              |     ||||     ||  |   |  ||  |     ||    || ||   || ||  ||  |  | |   | | ||   ||||  |||||   | ||  | | ||||| |||||||||||||| || |||||||| ||||||||||| |||||||| ||| | |||||||| |||||||  ||  | ||| |||| 
-------------ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttc--gttctggagcgtatagttt---tgttaagaattgattttg--gtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG-

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|298197159|gb|HO041902.1|HO041902
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|5606114|gb|AI900212.1|AI900212
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|254342930|gb|GR859092.1|GR859092
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|254334110|gb|GR849028.1|GR849028
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|298194561|gb|HO043033.1|HO043033
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|151411324|gb|EV281135.1|EV281135
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|192302734|gb|FG993754.1|FG993754
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|192297468|gb|FG992696.1|FG992696
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAGGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|51334757|gb|CO978623.1|CO978623
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|254334109|gb|GR849027.1|GR849027
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|298178531|gb|HO024266.1|HO024266
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|298163034|gb|HO011767.1|HO011767
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|298176675|gb|HO026796.1|HO026796
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|6567248|gb|AW234859.1|AW234859
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|192323071|gb|FK017012.1|FK017012
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctctctc ... gttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG
                                    atttgat  putative branch site (score: 5)
       taattcat  TA-rich tract