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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG

Basic information

species Glycine max
transcript GLYMA10G30400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
-gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
     ||  ||       |  || ||  | |||  | ||  | |  |  ||       | | |  ||||||    | || |        || ||  |||   |  |||  |  | |||||| || |||||||| ||||| || || ||||||||||| || ||| | |||||||| || ||| ||||||| || ||||| ||||| ||||||
gtccggctctctcttttttttttacatatttttactgttatatctcagcttagc----ctgagcttgttttatccatatcaa-------ttcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
----gttagccatcatgcacatcatttcaattatttgtttttggaccaaacattt-----atgat---gcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttc--------cagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
     |   | |  ||      || |||| ||  ||  |    |   ||  | ||      | ||   || |  ||| |||   | |  |  | |       ||| | | |  || | |||  ||         |||||| || |||||||| ||||| || || |||||||| || || ||| | || || ||||||||||||||||| || ||||| ||||| ||||||
gtatatatacaaatatat-tgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTA---ATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
                 | | ||  ||| | | || || |        ||     |     || |  ||  |  |  | |  | |    ||     || ||       ||  |  ||||| |||||||| || |||||||||||||| || || ||||| |||||||| ||||   ||||||||||||||||||| ||||| ||||| || |||
----------------gttagttagattttgttttcttcggtt-----ttcgcagttta-cggtttcttaaaacaagttaaaaaga---ttggattttttgt------ttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
                                           |  |  |  || | |   |    | ||    ||    ||  |     | |   |  ||          |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||
-----------------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg--------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
                                           |  |  | ||| | |    | |||| |    |     |  ||    | |  |  ||       |    |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| |||||||||||||| || 
-----------------------------------------gtagcctgtgatgtttcta-agttgttcttcccaaggatt--tggagctcactctctc-----gcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 1
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
                                           |  |  | ||| | |    | |||| |    |     |  ||    | |  |  |||           |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||
-----------------------------------------gtagcctgtgatgtttcta-agttgttcttcccaaggatt--tggagctcactctctctcttgg-----cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
                                           |  |  | ||| | |   |    | ||    ||    ||  |     | |   |  ||          |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||
-----------------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg--------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

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|6566810|gb|AW234442.1|AW234442
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|15814341|gb|BI786616.1|BI786616
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|19347182|gb|BM892062.1|BM892062
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|19348759|gb|BM893291.1|BM893291
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|26058273|gb|CA801187.1|CA801187
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|151403142|gb|EV272952.1|EV272952
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
EST: gi|192302446|gb|FG997358.1|FG997358
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTT
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTT
EST: gi|20813404|gb|BQ297882.1|BQ297882
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagccatc ... atttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
    ttttgat  putative branch site (score: 4)
                                            tatttttcc  putative PPT
                                  ttctgaaaaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA