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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacataatcatacctatgccgactttgtactaggtttatgttggattttcttgatagaatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT

Basic information

species Glycine max
transcript GLYMA15G08090.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 6
acacataatcatacctatgccgactttgtactaggtttatgttggattttcttgata---gaatac-atgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
    | |||        | ||  ||||  | ||  || |  | | | | |    |||   || |||  ||||  | |  | |   |  | ||||   |||| ||||||||||||||||||||||| |||||||| || |||   || || | |||||||||||||||||  || || ||||| |||||||||||||| ||||||
---tagaatttggaacttaccagcttttcattattttaagatcgcaatattgcaatatttgactactgtgttgagtctgactgtgtcatatcatggctatt-agGTTTTTGTGGAGGAAGAATGCTACTTTTGCTATCTCTCGGCACTACAAACGCTTTGATGTATTTGAAGAAGCAGAAGCTAATAAAGCTGCTGGCAAGTAT

upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 6
acacataatcatacctatgccgactttgtactaggtttatgttggattttcttgatagaatacatgtt--tcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
  |    |||||     | | ||| || || | |  | ||    ||   |   | |    ||  || |  |  | |   | ||| ||| |        |||||||  | |||||||||||| | ||||||||||| |||   ||||| | |||||||||||| ||||  || || ||||| || ||||||||||||||||| 
gtatcccatcattgtagtac-gacatt-tatttgactgatccatgaaagttgggctgctgtaagtgataatgagtaatctgatttctcactctacctgttagGTTCCTTTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTTGAAGAAGCAGAAGCGAACAAAGCTGCTGGAAAGTAC

upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
acacataatcatacctatgccgactttgtactaggtttatgttggattttc-ttgatagaatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
  |  | |||||  | || | |  ||| |   | | ||   |   | ||    || |  ||   ||      |||   | ||| ||  |        |||||||  |||||||||||||| | ||||||||||| |||   ||||| | |||||||||||| || |  || || ||||| || ||||||||||||||||||
gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataagg-agcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT

upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
acacataatcatacctatgccgac--tttgtactaggtttatgttggattttcttgatagaatacatgttt-cggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
     |  |   |  || |   ||  ||||   |  |      ||    ||  | | ||   | |  |  | | |||  |||| ||   ||     |  | || || ||||||||||| ||||| |||||||| || |||| |||||| | ||| |||||||| || || || ||||||||||||||||||||||| || |||
---agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT

upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
--acacataatcatacct--atgccgactttgtactaggtttatgttggattttcttgatag-aatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
     |||    ||   |  ||     || ||   |  | || |    | | |  || ||   |||  |||||| || || |||||    |  || ||| || |||||  |||||||||| ||||| | ||||||||| |||| ||||||||||||||||||||| ||||| || || || ||||||||||||||||  ||||||
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaat----cctattctt-ttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT

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|192297456|gb|FG989865.1|FG989865
EST:     CTTGATGGAAAGCTTGAGCTTGTTGTTGATCCATATCAAATCCTTGAAAG                         GTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACG
genomic: CTTGATGGAAAGCTTGAGCTTGTTGTTGATCCATATCAAATCCTTGAAAGgtatatctca ... ccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcttgatagaatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
                             cattaat  putative branch site (score: 3)
                                      ctctcatccttattt  putative PPT
                            acattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacataatcatacctatgccgactttgtactaggtttatgttggattttcttgatagaatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
acacata
- - - - - - - ctatgcc
- - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - atgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctctc