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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttggtctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag

Basic information

species Glycine max
transcript GLYMA14G04890.1
intron # 31
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 31
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 31
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttggtctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag
||||||||||||||||| |||||||| || || ||||||||||| ||||||||||   | || ||||| || ||| | |  || |||||    |   ||| ||  || |    |||   ||  ||||| ||          || ||    |       | || ||||        | |||| || ||| ||  ||  |  | | |||||  ||                                 
AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAGgtaatcagtgttggct--aataatggttt---ttgcgtacaattcaa-------aactggcaaga------aataatctga-------gtgtttaagatttaagagtgtaaata-tctgtttattt---------------------------------

upper sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 31
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 27
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttgg-tctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag
||||||||||| ||||| || ||||||||||||||||| ||||||||| |||| | ||| || |||||  | ||  | |  || ||||| ||   ||  | |||   | | || || |     |  |||   |  |  || |   ||||    ||  |   |||||||  |   || || ||  |  |     |                                                     
AGGAGAGATGTCTATGGAGCCTGGGAGCAGTATCTTGGTTTGGAGCATGCTGATACTGCACCAAAAAGGGCCTACACAGCCAATCAGgtatgctgct--gtctggttgtg-aacttgtgaagcgagcatagcgaattcttgtgcctgttacttttacct-ttattctgtca---ctcggcttgggcatatctat-----------------------------------------------------

upper sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 31
lower sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 20
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacat-tttggtctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag
 |||||||||| |||||||||||||| || || |||||||||||||| ||||| |   |  | ||| | || ||  |    || ||||| || ||   |        | | |||   |   ||||| || |||| | | |  |     ||   || | ||   || || |  |      || ||| |||    | |                                                   
CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAGgtatgcaatgctattctgttgtgaaatgagtg--aagtagatgtttgatgtgtcca-----tgaacttattcatggttttgtttgtgtcc--ttctagctttactctcg---------------------------------------------------

upper sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 31
lower sequence: GRMZM2G014805_T02 (Zea mays), 5'ss of exon 12
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttggtctttttaa--ttgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag
||||||||||| |||||||||||||| || || |||||||||||||| || || |   |  | ||||| || ||  | |  || |||||  | ||   |   | |    | ||  |   | || || || || | | || |||  |||| |  ||  |  | | |  ||   | |  | |      |                                                             
AGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAGgtaggcaatgctatattctgttgtaaaatgagtgaaataaatgttcgacgttgtaagattgtggaagtgcttgattgtattgcatagatggagcacatat-------------------------------------------------------------

upper sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 31
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 31
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttggtctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag
|| |||||||||||||||||||||||||||||||||||  | |||||| |||||| ||||||||||||  | ||||| | ||| ||||| |||  |||  | ||    |  || || |||   ||    || | | |  |  |||||     ||    | |  | | || |  |     |  ||                                                              
AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAGgtatgttgctt--cttg--gtattaacttctatcctgt----ttagatatgctagattgtaa--attccatattgatgttgtcacccaaccatgcag--------------------------------------------------------------

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|21677323|gb|BQ629674.1|BQ629674
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|208180635|gb|GD973780.1|GD973780
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|27427525|gb|CA939045.1|CA939045
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|5770494|gb|AI973668.1|AI973668
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|9565141|gb|BE474641.1|BE474641
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|58020429|gb|CX707171.1|CX707171
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|22523119|gb|BU081930.1|BU081930
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
EST: gi|207784911|gb|GD758228.1|GD758228
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAAGAAAGACCAGTAAAGATTTATAATTAGGAAACT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGA-GAA-G-CCAGTAAAGATTTATAATTAGGAAACT
EST: gi|7283882|gb|AW596484.1|AW596484
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG                         AATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaact ... tttgtttcagAATCGCCACACTTTCGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAGgtttgtaactttgcctgcaagagcaatttatattaagtacattttggtctttttaattgttgtggttgtccactattctggtaatactgggttttagttttgaggttgagagaactttgttttattacaccatttcaagttgcatgcgttttgtttcag

- - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT