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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatgtttgtgtgagaaaaatttacacaagtgcatatgattaaattcattctatcaagctaataatactattttttttctcttttttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA

Basic information

species Glycine max
transcript GLYMA15G09630.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09630.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G18040.1 (Arabidopsis thaliana), 3'ss of exon 2
-tatgatgtttgtgtgagaaaaatttacacaagtgcatatgattaaattcattctatcaagctaataatactattttttttctcttttttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA
 || | | | | |          ||||        | ||         ||||  |  |||   |||   ||   ||||| | | ||   ||     |  ||||| | ||| |||||||||| ||||||||||| |||||||||||||| ||||| ||||| ||  | ||| | | ||| ||||  ||  ||||||||||||
gtacggtttctattcttct----tttattttgactcgtaactcctgcgtcatcat-ccaattgaatctcaccggtttttct-ttttacatgcttggtttagTTGCTTGCATTGATTGGAGAGCAGTTTGATCATGGAGATGAAATATGTGGAGCAGTTGTCAACATTAGAGGAAAGCAAGAAAGGATATCTATTTGGACTA

upper sequence: GLYMA15G09630.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g02250.t01 (Vitis vinifera), 3'ss of exon 2
tatgatgtttgtgtgagaaaaatttacacaagtgcatatgattaaattcattctatcaagctaataatactattttttttctcttttttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA
                | |   ||||  |  || || |   || |  |    |  | ||  |  ||||     || |  |||    | | | | | | ||||| | || ||||| ||||||||||||||||| ||||||||||| || ||||| ||  | |||||||||  ||| ||||| ||||| ||| | ||||| |
----------------gtatgctttaggct-gtacagaaattttatgttgagcc-ttaaatttttaatgtggcttctaatcttcaatatatgc-tactagTTGCTAGCCATGATCGGAGAACAGTTTGATCATGGAGATGAAATCTGTGGAGCAGTGATCAATGTCAGAGCTAGACAGGAGAAAATAGCTCTATGGACCA

upper sequence: GLYMA15G09630.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S426_46V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------tatgatgtttgtgtgagaaaaatttacacaagtgcatatgattaaattcattctatcaa--gctaataatact---attttttttctctttt---ttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA
                                                                                    |  |||| |    || ||      |   |   |  |||    || |||| |||||  | ||   | | |   | | || || | || |   ||||   |||| |||| |||| ||||||||||| || |||||  | || |||||||| ||||||||||||||||  || || ||    || || || ||||| || ||||| |
gtactgtctatctttcttgattctgggttttcctactgtcgctttggttgaatatgtcctcatggaaatagggaaagttggtcaacttttgagctgaaacaagcgctccgcatatctgagatagttttgattcgatcaattgatatctagatttgaagtcttattatattgtaatttgtgggttca-gTTGCTGGCTATGATTGGAGAGCAATTTGACGAAGGTGATGAAATTTGCGGAGCTGTTGTGAGCGTAAGGAGGGCACAAGATAAGATTGCCATCTGGACGA

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|213613945|gb|DB960938.1|DB960938
EST:     GGACTATGACCTTCCAAAGGGGAAAATATGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAG
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAG
EST: gi|298194469|gb|HO042941.1|HO042941
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGA
EST: gi|31457012|gb|CD399040.1|CD399040
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|18735078|gb|BM528551.1|BM528551
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|192308366|gb|FK002794.1|FK002794
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|9820397|gb|BE555907.1|BE555907
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCNGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|15337801|gb|BI498457.1|BI498457
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|6846595|gb|AW348885.1|AW348885
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|207826521|gb|GD798652.1|GD798652
EST:     GACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|6724495|gb|AW308894.1|AW308894
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|209698255|gb|BW678026.1|BW678026
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|298191604|gb|HO039083.1|HO039083
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|298165619|gb|HO011668.1|HO011668
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCAC
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCAC
EST: gi|31470645|gb|CD412673.1|CD412673
EST:     GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTCATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: GGACTATGACCTTCCAAAGGGGAAAATCTGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
EST: gi|209698256|gb|BW678027.1|BW678027
EST:     TGATACCAGTTGGTTATATACG                         TTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA
genomic: TGATACCAGTTGGTTATATACGgtatcgtttt ... tcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattctatcaagctaataatactattttttttctcttttttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA
             agctaat  putative branch site (score: 3)
                      tactattttttttctc  putative PPT
                taataatactattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatgtttgtgtgagaaaaatttacacaagtgcatatgattaaattcattctatcaagctaataatactattttttttctcttttttgtcccttcaagTTGTTGGCAATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGCGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGAAAAAATTGCTATTTGGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT