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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaaggcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG

Basic information

species Glycine max
transcript GLYMA20G38630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 3'ss of exon 3
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaaggcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
|||    |       |  | |   | |  || |       | | |        |   | |   |  ||      |   | || |    | |     |||||||||||| |||| |||||||||||| || || ||| | |||||||| |||||||| || || ||||||||||| || |||||||||||| |||| ||||
taatggctcacctcgttttgcgtatcttcctaatctcctcaatcccctcctcctcaaacacaccctaagtattttcacatatttttcctctatgccatagGATGATTCAGAAATAGTTGCAATGATAAAAGAGTTGCTGGAGACTCGCATTCGACCAGCTGTTCAAGATGATGGTGGTGACATTGAATATCGAGGATTTG

upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 3
taagactttgtaaaatggtccaagtttgtcttac-tcatgg-agtacataggaagtttgagaaggcg-aaaactaaatggta-catatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
   |||    || | |  || || |  || |||  | |||   |    ||      ||| | ||  |  | ||| |||  |  | |  ||  ||| ||   |||||||||||||||| |||||| ||||| || ||||| || |||||||| |||||||| || || |||||||| ||||| |||||||||||  |||| || |
--tgacaacatacatt--tcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG

upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 3'ss of exon 3
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaaggcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
         |||   || | | | | | |  ||  | | || |          ||| | ||| | || |||||    |        ||| || |    ||||||| |||||||| || |||||||| |||||| | || ||||| || || |||||  |||| ||||||||||| |||||||| || ||| | || || |
---------gtaggctgctgccaatgtttgctagacttagact----------tttaaaaagccaaatactaatcaatg-------attgtttctc--agGATGACTCTGAAACTGTAGCAATGATTAAGGAACTCTTGGAGACGCGTATCCGACCATCAGTCCAAGATGATGGAGGGGACATCGAGTATTGTGGATTCG

upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 3
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaag-gcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
 ||   | || ||     |||||| || |  ||   | |       |   |||| | |     || |   ||   |  |   |  |  ||||   ||  ||||||| ||||||||||| ||||||||||||||| | ||||| || || ||  |||| ||||| ||||||||||| ||||||||||| ||| | || ||||
-aacgttctgcaatgctctccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG

upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtt-tgagaaggcgaaaactaaatggtacatatacatttttccat-atagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
|   |||    |||||| |  |         |  ||     ||    ||  | |  ||   |      |  || ||      |     | || |||| | |||||||||||||||| || ||||||||||| ||| |||| |||||||| |||||||| ||||| ||||||||||| |||||||| || ||| | || ||||
tggaactcc--aaaatgtttaattccaaatattttctgattgtctgcagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG

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|208326189|gb|GE121985.1|GE121985
EST:     TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAA                         GATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
genomic: TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAAgtaagcatgc ... ttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
EST: gi|151408856|gb|EV278664.1|EV278664
EST:     TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAA                         GATGATTCTGAAACAGTTGCGATGATCAAGGAATTGTTAGAGACTCGAATT
genomic: TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAAgtaagcatgc ... ttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
EST: gi|298169495|gb|HO020855.1|HO020855
EST:     TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAA                         GATGATTCTGAAACAGTTGCAAT
genomic: TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAAgtaagcatgc ... ttccatatagGATGATTCTGAAACAGTTGCAAT
EST: gi|213591380|gb|DB959894.1|DB959894
EST:     TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAA                         GATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
genomic: TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAAgtaagcatgc ... ttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
EST: gi|192327952|gb|FK021699.1|FK021699
EST:     TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAA                         GATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT
genomic: TCTTTTTAGATTCTCAAGCCGCCGCGGCCATGGATACAGCTATTCACCAAgtaagcatgc ... ttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggaagtttgagaaggcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
                      aactaaa  putative branch site (score: 2)
                                        catttttcc  putative PPT
                                tacatatacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaaggcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -gactttg
- - - - - - - - - - - - - - - - -ctcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatac