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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattgctcaatcatttatttatgccaaacagtcagtcttcattcatataaacatatcacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA

Basic information

species Glycine max
transcript GLYMA06G17050.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 9
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 8
gtaaatattgctcaatcatttatttatgccaaacagtcagtcttcat----tcatataa----acatatcacattttaac-ttgagt--tttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
||   | ||       ||  |  |  || | |    |||   ||||     |  ||| |    | ||||    |||| |  ||||    || ||||||||| |||||||| ||||| ||||| ||| |||| |||||||||||   ||||||||| ||||||  ||||||  | || ||||| || ||||| ||||
gtgtgtcttatgttcccagatgatagtgtctattcatcatgattcacataattgtatgatagtaaatatttttttttcatgttgacctcttcacagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGAAGTCCTTCAGCTGAACGTCGGGTTAATCTGTCAAGCATTA

upper sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G136296_T03 (Zea mays), 3'ss of exon 9
-----gtaaatattgctcaatcatt-tatttatgccaaacagtca-gtcttcat-tcatataaacatatcacattttaacttgagtt--ttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
         | |||   | || |   | | ||| |   |   |||  |  |  | | |||  |||   |    ||  |  ||||  |  |  |||||||| |||||||| ||||| ||||| ||| |||| |||||||||||   ||||||||| ||||||  ||| ||  | || ||||| || ||||| ||||
gtgtgtcttacattctccgatgacagtgtgtattcatcatgttcacataattgtatgatagtaactattttttttccatgttgatctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA

upper sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 9
gtaaata-ttgctcaatcatttatttatgccaaacagtcagtcttcattcatataaacatatcaca-tttta----------acttgagttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
||   || ||| ||||     |  ||| |  || |    |   || ||  ||  ||   || |  | |||||          | |||   |||  |||||||||||||||| ||||| ||||| ||  |||| |||||||||||  | ||||  || || ||  |||| ||  | ||||||||||| || ||||| |
gtgggtagttggtcaacataatgcttacgtaaatc--ctatcttttataaatggaattttaccctaattttatgtccatctcatttggcctttttagGTGGTTGAGGTTGTAAGTGGGGATTGCATCATTGTAGCTGATGATTCTCTCCCATTCGGCAGCCCATTAGCAGAACGACGAGTTAACCTCTCCAGTATCA

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|7233337|gb|AW568684.1|AW568684
EST:     CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAG                         GTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATT
genomic: CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAGgtaaatattg ... agttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATT
EST: gi|207759067|gb|GD733510.1|GD733510
EST:     CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAG                         GTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCAAA
genomic: CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAGgtaaatattg ... agttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCA--
EST: gi|7233314|gb|AW568661.1|AW568661
EST:     CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAG                         GTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATT
genomic: CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAGgtaaatattg ... agttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacagtcagtcttcattcatataaacatatcacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
                                   ttttaac  putative branch site (score: 2)
                   atataaacatatcaca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatattgctcaatcatttatttatgccaaacagtcagtcttcattcatataaacatatcacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGATTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG