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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattttgcctcaagattttggtcttctgaatactgctctgttttttttttcttttaaatgtttgacatagcac...

Basic information

species Glycine max
transcript GLYMA17G05130.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05130.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 5
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattttgcc-----tcaagattttggtcttctgaatactgctctgttttttt--tttcttttaaatgtttgacatagcac
||||| ||| | | ||||| || ||| || |||| ||||||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||| | | ||| || || | || ||| | | | || | || || | | || ||| | || |||| | |||
GTAACATTTGTGAACAAGGATGGCACAGAGCAGACAATCAGTGTCCCTGTTGGAATGTCCATCTTAGAAGCTGCTCATGAAAATGACATCGAACTTGAAGgttactgatttatcattgcaactgtactatgctttcaattcttaacttcttttgctgataagaacagctataaaaagcaaattatgtttacccaatagac-------

upper sequence: GLYMA17G05130.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 5'ss of exon 4
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattt-tgcctcaagattttggtc---ttctgaatactgctctgttttttttttcttttaaatgtttgacatagcac
|| |||||| |||||||||| || ||||| |||| | | ||||| ||| | |||||||| ||| |||| || || ||||| || ||||||||||| ||||| | || | | || | || | ||| | | ||||| || || | | ||| | || || | | || ||| | | | |
GTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAACTTGAAGgtca---tttgaaatgccgagtcttaatgtttgctcattttgatttaaatcaatttttaagtacatttatgcttgtgcatgtttcatgttgtgttggacaaaa-

upper sequence: GLYMA17G05130.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G013607_T02 (Zea mays), 5'ss of exon 5
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattttgcctcaagattttggtcttctgaatactgc--tctgttttttttttcttttaaatgtttgacatagcac
||||| ||| | | ||||| || || ||| || || || ||||||||||| |||||||||||||||||||||||||||||||| || ||||| | || | | | | || || | | |||| | ||| | || || ||| | || | ||| | | | | |
GTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAGCTTGAAGgtacagatattaagga-aatgtgcacttcccttccactgtggtttttgcctttatggttctatagtcagttcatgcttggtgataagaatat-atgcacctt

upper sequence: GLYMA17G05130.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G856338_T01 (Zea mays), 5'ss of exon 1
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgatttta-gaattctattattttgcctcaagattttggtcttctgaatactgctctgttttttttttcttttaaatgtttgacatagcac
||||| ||| || | ||||| || || ||| || || || ||||||||||| ||||||||||||||||||||||| |||||||| || ||||| | | || | | || |||| | | || || | | | | || ||| | || | ||| | || |||| |
GTAACATTTGTTAACAAGGATGGCTCAGAAAAGACAATACGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAATGACATAGAGCTTGAAGgtacaaatattacaaagatgtgcacttctattctagtgtgggtattgtgtttatggttttgtagtcagttcatgcttggtgataagaatatgtcata-tat

upper sequence: GLYMA17G05130.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 5'ss of exon 5
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattttgcctca-agattttggtcttctgaatactgctctgttttt--tttttcttttaaatgtttgacatagcac--
|| | ||| |||||||||| || ||||| | || || | ||||| |||||||||||||||||||||||||||||||||| || |||||||| ||||| | |||||| | ||| | |||| | || | ||||| | | || || | | ||| | || || || | | | || ||||
GTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAACTTGAAGgtgtgtattttgat----gcatttt-ttatcgtatcttgcacattttccttgacctcattttgttttttttataattattattcttagcatgatgcacagcattt

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|10231340|gb|BE800228.1|BE800228
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|192322757|gb|FK014448.1|FK014448
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|254345030|gb|GR855687.1|GR855687
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|6070770|gb|AW100157.1|AW100157
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|298179386|gb|HO027857.1|HO027857
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGCTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
EST: gi|14259415|gb|BG882323.1|BG882323
EST:     TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAG                         GAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG
genomic: TGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctt ... gttattgcagGAGCATGTGAAGGATCGATTGCGTGTTCAACTTGCCATGTTATAGTCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAACTTTTATTGATAAGGACGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAACGACATAGAACTAGAAGgcaagagctttgattttagaattctattattttgcctcaagattttggtcttctgaatactgctctgttttttttttcttttaaatgtttgacatagcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT