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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcatatgatctcattcccaacccaattctgctttttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG

Basic information

species Glycine max
transcript GLYMA13G44910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
gtcagtcatatgatctc-attcccaacccaattctgctttttaatttcattcttccaaat-cctatgcatttcttaattgtgatgttt-tat-cttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
     | || |  | ||   | |     | ||  |  |    ||  |   ||| | | ||   ||  | || |   ||| |  ||||| ||  ||      ||||||||||| ||||||||||  || |||||  ||||||| || || |  |||||||| || || || ||||| ||||||||||| ||||||||||||||||
----tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG

upper sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
-----gtcagtcatatgatctcattcccaacccaattc--tgctttttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
     |   ||||  | |     ||   | |  | ||   ||  ||||| |  |||||    | ||  | |  |  |  || |   | |   |||| | |    ||||||||||| || ||||||||||| |||||  ||||||| |||||||  || ||||| || || ||| |||| |||  |||||| ||||| ||||||||||
ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattca---atattttgtcaaggttctactaaaggttccttatttac----cagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG

upper sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtcatatgatctcattcccaacccaat---tctgctttttaatttcattcttccaaa---tcctatgcatttcttaattgtgatgttttatcttcacctc--agATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
          |  | |  || || |   |||   |  | |   | | |  |||  || |     || ||     || |    ||  || |||   |||  | |   |||| ||||| || ||||||||||| ||||||  |||| |||||||||| || || ||||| |||||||| || ||||||||||| ||||||||||||||||
--------agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG

upper sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtcatatgatctcattcccaacccaattctgcttt-ttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
     | | || ||  | |  | || |||||   | ||  | || || ||| |   |      |     ||     | |  ||| | |   |     | |||| ||||| || ||||||||||| ||||||  |||||| ||||||||||| |||||||| ||||||||| | ||||||||||| || |||||||||||||
actgctaaaattatgac-tcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG

upper sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
gtcagtcatatgatctcattcccaacccaattctgctttttaatttcattcttccaaatcctatgcatttcttaa-----ttgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
   | ||   | ||||   | || |   |||     |   | | |   ||     | | |  |||  ||  | ||     | || ||   || | || |    || ||||||| || ||||| || || |||||||||||||| |||||||| || || ||||| || |||||  | ||||| ||||| ||||| ||||||||||
---actctgttcatctgtgttcccatgaaatatatttgcctgagtgtgttgcaa-acaccacatgacttaatgaaaaccttggtaattgcttgt-ttaattgaagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATG

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|193542174|gb|FK497476.1|FK497476
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|192315478|gb|FK007796.1|FK007796
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|298173138|gb|HO020122.1|HO020122
EST:     AGACTCTGAAAGGCAGCCACTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|193710246|gb|FK645506.1|FK645506
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAA
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAA
EST: gi|192315477|gb|FK007795.1|FK007795
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|298191541|gb|HO039020.1|HO039020
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|193476729|gb|FK439562.1|FK439562
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGAC
EST: gi|193323635|gb|FK290487.1|FK290487
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
EST: gi|192307602|gb|FG999641.1|FG999641
EST:     AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACT                         ATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC
genomic: AGACTCTGAAAGGCAGCCATTTCGAAATCAGGGTTCAGCCCTCAGACACTgtcagtcata ... ttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
                        tcttaat  putative branch site (score: 3)
                                      ttttatcttcacctc  putative PPT
                     atttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcatatgatctcattcccaacccaattctgctttttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG