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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctttttcatcccattttttctgtcttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC

Basic information

species Glycine max
transcript GLYMA06G15350.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 13
gtttgctttttcatcccattttttctgtcttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
|||||    | ||  |  || ||  ||     |   ||||  |     || |  |   | | |  | |    ||  |||| ||||| || |||||||| || |||||||||||||| ||||| ||||||||||||||  | ||| ||||  |  | || |||||||| || ||||||||||| 
gtttgtaactaca--ctgttcttagtgctcgtgctcactacag----gtgcttatgattgattttgtt-taattcttttccagTGGGGAGTTTGTTGTGGTTAACAAGCATCTTCTCCATGATTTGACTGAAATGGGTGTTTGGACTCCAGCTCTGAAAAATAAGATAATTTATGAAGATGGT

upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 13
--------gtttgcttttt------catcccat--tttttctgtcttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttc-tagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
         | ||||  ||      | | | |   || || ||  |   || | | |||||      |  |   ||||  | ||| | |   |||   ||||| || |||||||| || |||||||||||||| ||||| |||||||| |||||  | ||||| |||    | || || |||||| ||||||||||||| 
gtctgcaaatctgctccttgttaaacgttcaaccgttgttttggttacatgaatttttgccagtctgttttggtttacatgactagtttccttttggcagTGGCGAGTTTGTTGTAGTAAACAAGCATCTTCTCCATGATTTGACTGAGATGGGTATTTGGTCCCCTGTTCTGAAAAACAAGATTGTCTATGAAGATGGT

upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 13
gtttgc--tttttcatcccattttttctgtcttggtgtactattgcct-catgatcctatcttactgggcta-ctgtttgt-ttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
|| ||      | |     | || ||  |  |   |  | | |  | | ||||  | ||| | | ||  ||  || ||| | ||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||||||  | ||| |||||||  | || ||  |||| || ||||| ||||| 
gtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT

upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 13
gtttgc--tttttcatcccattttttctgtcttggtgtactattgcct-catgatcctatcttactgggcta-ctgtttgtt--tctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
|| ||      | |  || | || ||  |  |   |  | | |    | ||||  |  || | | |   ||  || ||| ||  || ||||| ||||||||||| || ||||||||||||||||||||  |||||||||||||  | ||| ||||||| || || ||  |||| || || || || || 
gtctgtaacaatactccctacttctttagggtgtttacattgtgatgtacatgtgcacatgtgattaatctttctattttttgttccagTGGGGAATTTGTTGTGGTCAACAAGCATCTTCTTCATGATCTGACTGAAATGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGT

upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 13
gtttgctttttcatcccattttttctgtctt----ggtgtactattgcc-tcatgatcctatcttactgggctactgtttgtttct-agTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
||||| |||   | || |   | |   | ||    | | || || |    |    |||  |   | ||       ||||| ||| | ||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||  | |||||  |||| || |||||  |||||
gtttgttttgctaccctaacctgttcattttctaagatttagtacttttgttgccatctaagtctcctctttccttgtttctttgtcagTGGTGAATTTGTTGTGGTAAACAAGCATCTTCTTCATGACTTAACTGAGATGGGTCTTTGGTCACCTACTCTTAAGAACCAGATAATTTATGAGAATGGC

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|208153189|gb|GD949202.1|GD949202
EST:     GAGTGTTTTGACCCATATACTTCAAACATATACAGTCGTAGAGTTTTAAG                         TGGTGAATTTAGTTTGTTGTGAACAAAGCATCTTCTTC
genomic: GAGTGTTTTGAACCATATACTTCAAACATATACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTT-GTT-GTTGTGAACAA-GCATCTTCTTC
EST: gi|207810107|gb|GD780881.1|GD780881
EST:     TGTTTTGAACCATATACTTCAAACATATACAGTCGTAGAGTTTTAAG                         TGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT
genomic: TGTTTTGAACCATATACTTCAAACATATACAGTCGTAGAGTTTTAAGgtttgctttt ... ttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC
                           atcttac  putative branch site (score: 3)
                                            tttgtttct  putative PPT
       tactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctttttcatcccattttttctgtcttggtgtactattgcctcatgatcctatcttactgggctactgtttgtttctagTGGTGAATTTGTTGTTGTGAACAAGCATCTTCTTCATGACTTGACTGAAATGGGACTGTGGTCTCCTACATTAAAGAATAAGATTATCTATGAAGATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG