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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG

Basic information

species Glycine max
transcript GLYMA18G49770.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 3
-----------gtaggattgtttactattt-tgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttc--------tgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
             ||  ||| | | | ||| | || | || |    | |||||     ||   |   | | ||||||         |||| || |||  |||| || ||||| || || || || || || || |||||||||||| | ||| | ||||| |||||  | ||||||||||||||||| ||||| |||||||
gcttccgcattacagatttggtaattttttatatgcattgtactgatatgcttcagttag-catccgaggataattttcttttgtttgatctttgaattagATCATATCTGGTGTTGAATATTGCCATAGAAACATGGTGGTTCATCGTGATCTTAAGCCAGAGAACCTTCTTTTGGACTCCAAATGCAATGTTAAGATTG

upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------gtaggattgtttactattttgtgtagtgaa--gacttttgcttgtcacagatttttca-agctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
                   ||  |   | ||   ||    | |   |   || |||   || |    ||   || | |  ||  | ||    || || | ||||||| || || ||||| ||||| ||  | || ||||||||||| |||||  | |||||||| || || ||||||||||| ||||| ||||| |||||||
gtatgtttttattttattttatcaacatgtaactttccaagcaaccattcgattttatattatatttgagagttaagaattagctacttggctttgatgtagATAATATCAGGAGTGGAATACTGCCATCGAAACATGGTGGTTCACAGAGACCTCAAGCCTGAAAACTTGCTTTTGGACTCTAAATGCAATGTAAAGATTG

upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaggattgtttactattttgtgtagtgaagacttttg---cttgtcacag-atttttcaagctaatttctgattttgg-------------aagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
    | |||||| || |||    ||   |     ||||   | | |||    || ||| |   | | |  || || ||               |  ||||||| ||||| || |||||||| ||  | |||||||| || ||||||||  ||||||||||||||||||| ||||| || |  |||||| | |||||||
----gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG

upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------gtaggattgtttactattttgtgtagtgaagacttttg--cttgtcacagatttt--tcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
                                              ||   |  | |    ||  |  |||   || ||   |   || | ||||   |   |  ||||  |    |    | |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||| | || |||||||| || |||||||| |||||||| ||||| |||||||
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcct---gaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG

upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagct--aatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
                        | | ||| || |  ||| ||||| ||     || |||||  |||    ||| ||  |    |||| || ||  ||   ||||||  | ||||| ||||| || || ||  |||||||||| |||||| | || |||||||| ||||| |||||| | ||||||||||| || |||||||| |
aggtaaattccttggttgtttgaatggaatttttgaggattctgtgtggtc----ctcttgctcttcaggcttttatctggtataaattgctcatgctgc--gcagATTGTGTCTGGCGTGGAATATTGCCATCGGAATATGGTTGTTCATCGTGACTTGAAGCCAGAGAACTTACTTCTCGACTCCAAATGGAACGTCAAGATAG

upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 2
gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
                      ||   |    | || || ||    |||    | ||  ||| |   |        | ||||| || ||||| ||||| || |||||||| ||||||||||||||| | ||| ||||||| || ||| |  |  | ||||| |  || ||||| |||||||
----------------------gtt-cgtgctccttcgcctggtgaagaaaactgaatataactc--gcacacatcaccagATCATTTCTGGAGTGGAATATTGTCACAGAAATATGGTGGTTCATCGTGATCTGAAGCCAGAAAATCTGTTGCTTGACTCTAGGTGCAATGTGAAGATTG

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|209729574|gb|BW651888.1|BW651888
EST:     TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG                         ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
EST: gi|27445912|gb|CA953035.1|CA953035
EST:     TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG                         ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAAAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
EST: gi|254315447|gb|GR825256.1|GR825256
EST:     TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG                         ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
EST: gi|192308573|gb|FK002469.1|FK002469
EST:     TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG                         ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
EST: gi|254336679|gb|GR842858.1|GR842858
EST:     TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG                         ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
                                     ttctgat  putative branch site (score: 3)
                                 taatttctgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC