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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctttccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag...

Basic information

species Glycine max
transcript GLYMA08G33830.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 5'ss of exon 4
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctt--tccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag
||||| |||||||||||||| ||  | |||||||| ||| | || || || ||| || ||||||| || ||||||||  | ||||||||||||||||||||| |||    | | |       |  | || | | | |     ||  | |   | |  ||      |     ||   |      |    | | || || |   
AACAAAGATGGATATGTCAGTAAGGAAGAGATGGTTCAATCAATGAATGAGACTGCAACAGGGGAACGCTCTTCTGGGCGTATAGCCATGAAAAGATTTGgtaagtcgcttgttctccagctctctggtctctgagtttagggcgaaaacaattagttgtatgcccttagatgtacatgttatgaataaattatattttt--

upper sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 5'ss of exon 4
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctttccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag
||||| ||||| ||||||||||| ||||||||| | ||||| || |||||||| |    ||| || || ||||||||  | |||| |||||||||||||||| |||| ||| |    |    |        |  | ||||| | | | |  || |    || | | | |  || | ||||     |  |  || |  |||
AACAAAGATGGGTATGTCAGCAAGAATGAGATGATACAAGCGATCAACGAAACCATCGGAGGAGAACGCTCTTCTGGGCGGATAGGCATGAAAAGATTTGgtaagttttcttttttgtggtatcgtcacaaatctcacatgaacaca-gtacacactgacaatgatggtc-ctaatacac---tcttttggtggtcccag

upper sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G006790_T01 (Zea mays), 5'ss of exon 3
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctt--tccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag--
|| || ||||| ||||| |||||  |||||||| ||||||| |||||||| || ||  |||| ||||| ||||||||    |||||||||||||||||||||||||| ||| |  |||  |  || | |   ||     | |   | |||  | |||  | ||  ||   ||| ||  |||      | |  |   ||  ||  
AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttctatttcttggtagctctatacctactagtcttttgtgtaaagt-aaaccacca--catttttggttggacaactctcttcctac-ctactagtc

upper sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G155822_T01 (Zea mays), 5'ss of exon 4
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctttccctttgtgtgtaaataaca-----tgcatataagctca-aatgagcattcaagcttgcttaaacacaggcatactcatgttatcag
||||| ||||||||||||||||| |  |||||| | ||||| ||||| || ||||    ||| ||||| ||||||||  | |||| |||||||||||| ||| |||||||||  |  |  || |  |    | |    |     |||   ||   ||  ||| |  |    || | ||||  ||     |   |  | ||      
AACAAAGATGGATATGTCAGCAAGAGCGAGATGATACAAGCAATAAATGAGACTATTGGAGGAGAGCGCTCTTCTGGGCGCATAGGCATGAAAAGATTCGgtgagttatctcctctgtcaccgtcatccacacaccctaatttctgctcttagtttcttaataaaaaggtcagttggctttcactacaaccctcatacgt------

upper sequence: GLYMA08G33830.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 5'ss of exon 4
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctttccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttat-cag
|| |||||||| ||||| ||||| |  |||||||| || || ||||| ||||| ||  |||||||||||||||||||||||||||||||||||||||| |||||||  ||   | || |  |  | | |  | | |       |  |  | |  | |   ||   |  ||   || | ||    || ||  |   || | |
AATAAGGATGGTTATGTGAGCAAGAGCGAGATGGTGCATGCAATAAATGAAACAACTGCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTCGgtcagtcctcctcctctctatcactttct-catacagtggctttgcacacactcacggatatgtgaatttatatatagacccagattctttttcaatactg

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|18735235|gb|BM528647.1|BM528647
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|18038716|gb|BM307010.1|BM307010
EST:     CTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: CTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|254316174|gb|GR827711.1|GR827711
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|207762743|gb|GD732974.1|GD732974
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|13563522|gb|BG551742.1|BG551742
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|14991862|gb|BI317535.1|BI317535
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|192305727|gb|FG995697.1|FG995697
EST:     AACTACATCAGGGGAGCGTTTTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|22524377|gb|BU083188.1|BU083188
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|13481965|gb|BG511308.1|BG511308
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|7590643|gb|AW706391.1|AW706391
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|19345846|gb|BM890726.1|BM890726
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAGGATGGATATGTCAGCAAAAATGAGATGGTCCAAGCTATAAACGAAACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatctctccctttccctttgtgtgtaaataacatgcatataagctcaaatgagcattcaagcttgcttaaacacaggcatactcatgttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA