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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag

Basic information

species Glycine max
transcript GLYMA04G42720.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag-----------
 | ||||| ||| | ||||||||| | |||||||||||  |||||||||||||||| ||||| ||||||||  ||||| | |||||||||||||||||||||||   | | ||   |   ||||   |     | |||||| |      |  |||    |  ||   || |    |           
TCCGGTACGTATGACAAGAATATTAAAGAGTGGCCACAACGAGGTGGAGCTAATGGAAGCTTGAGATTTGATGTTGAGTTAAAACATGGAGCCAATGCTGgtaacattaccttt--tcacgatttcgtttccttgttgcttgtaagtgtactttcagcaactaaaaatcctgattgaattattgaag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G120517_T03 (Zea mays), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgat--------tcattaaatattg-attatttccgaattttgcttatggagta-atattccctga-tgaattgtcatatcag-----------
|||||||| ||| | |||||||||||||||||||||||  |||||||||||||||| || |||||||||||  ||||| |||||||||||||||||||||||| || |        ||  | | |||   | |||    |  || | ||| |  |||  | | |   | | || |   ||  ||  |           
GCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttacttgacttctctcagtatcatactatcattgttttattcttctaaagtgtacaattagtaactgcaacctctgattggaattttaaaag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G006791_T01 (Zea mays), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatg---gagtaatattccctgatgaattgtcatatcag-----------------------
 ||||||| ||| | ||||||||| |||| ||||||||| |||||||||||||||| || ||||| || ||   ||||||||  |||||||||||||| |||| |   |  ||   |  |  |  || | ||||||  |    |    |  || || | ||  |  ||    | | ||                        
TCTGGTACCTATGACAAGAATATTAAGGACTGGCCACAGCGAGGTGGAGCTAATGGAAGTTTAAGGTTCGATGCTGAGCTGAGTCATGGAGCCAATGCGGgtatttcctactttcttgctagtggttgc-gaatttcacagtggcttaaaaaaaatcctcttgtctatc-cgacaccaaaacataggtctaaggtctagttt

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G014397_T02 (Zea mays), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattg--tcatatcag
|||||||| ||| | ||||| |||   ||||||||  || | |||||||||||||||||||| ||||| ||| | ||| |||| ||||| ||||||||||||||  | ||||   || || || || |   | ||      ||| |||  |  | |   |    |||  ||||  |||
GCTGGTACATATGACAAGAACATTACCGAGTGGCCCAAGTGTGGTGGAGCTAATGGTAGCTTGAGATTCGAAGTCGAGTTGAAGCATGGGGCCAATGCTGgtaac-actcatctcatctt-atcatctgtaacttc-----atgaagtggtgctgctcaacattttgtttcatgacag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G557799_T01 (Zea mays), 5'ss of exon 4
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatt-tccgaattttgcttatggagtaatattccctgatgaattgtcatatcag
|||||||| ||| | ||||| |||   ||||||||  || |  |||| |||||||||||||| |||||| || | ||| |||| ||||| ||||||||||||||   |    | |   |  |||||   | | |  ||  | |||  |   || ||     |   || ||||  |||
GCTGGTACCTATGACAAGAACATTATCGAGTGGCCCAAGTGCAGTGGCGCTAATGGTAGCTTGAGATTTAAAGTCGAGTTGAAGCATGGGGCCAATGCTGgtaacactcttctcagctt--attatcacctgtaacttcatgatgatgggttactcaacattttgtt-tcatgacag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G332922_T01 (Zea mays), 5'ss of exon 4
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgat-tcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag
|||||||| ||| | ||||| |||   ||||||||  || |  |||| ||||||||||| || |||||| || | ||| |||| ||||| ||||||||||||||   | | || |  |  | || |  |   | ||    | |||  |   || ||     |   || ||||  |||
GCTGGTACCTATGACAAGAACATTATCGAGTGGCCCAAGTGCAGTGGCGCTAATGGTAGTTTGAGATTTAAAGTCGAGTTGAAGCATGGGGCCAATGCTGgtaacactcttatcagcttattatcacctgtaacttca--tgatgatgggttactcaacattttgtt-tcatgacag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: AT4G08390.2 (Arabidopsis thaliana), 5'ss of exon 2
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag----------
|||||||| ||||| ||||| ||| |||| |||||||| ||||||||||||||||| || || ||||| || |||||||| |||||||  || || |||||||   ||    |  |||   |||||| | || ||    ||||  |||  | | |  | | | |||||  | |  |          
GCTGGTACGTATAACAAGAACATTAAGGAATGGCCACAAAGAGGTGGAGCTAATGGAAGTTTGAGATTCGATATTGAGCTTAAACATGCTGCTAACGCTGgtacctataagctttatacc-attattac-gagttagtgttatttagttgtttgctataa-gcattgtt-tgttggttgttattag

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G77490.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgatt----cattaaatattgattat---ttccgaattttgctta-tggagtaatattccctgatgaattgtcatatcag
|||||||||||||| |||||||||||||||||||||| |||||||||||||||||| ||  | || |||||   |||||| || ||||  || |||||||||| || ||    ||||  | ||  ||| |   ||  || ||||  ||  ||   | ||||||     |  |   | | |    
GCTGGTACTTATAACAAGAATATTGAGGAGTGGCCACTGAGAGGTGGAGCTAATGGAAGTCTTAGGTTTGAGGCTGAGCTTAAGCATGCTGCAAATGCTGgtactggtttcatcatttcacatgcattgtggcttaagacttttatttggtgtcttgatattctacttttgacatttacag---

upper sequence: GLYMA04G42720.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g02470.t01 (Vitis vinifera), 5'ss of exon 3
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag
|| ||||||||||| ||||| |||||||||||||| |  ||||||||||| ||||| ||  | |||||||||||||||||||||||||| |||||||| ||||||| ||      | |||| ||||     | ||| | | |  ||  | | | | |  |  |  || ||| ||||
GCAGGTACTTATAACAAGAACATTGAGGAGTGGCCTCTAAGAGGTGGAGCAAATGGAAGTCTGAGATTTGAAATTGAGCTGAAACATGGGGCCAATGCAGgtaatggtttg----acattgtttataatttagtttggttgacaga-cattgtcctc--acaatctggcatctcag

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|192296349|gb|FG991587.1|FG991587
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|207747581|gb|GD720258.1|GD720258
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|298189048|gb|HO035685.1|HO035685
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|298167788|gb|HO013051.1|HO013051
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|10233020|gb|BE801908.1|BE801908
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|12689032|gb|BG155377.1|BG155377
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|11274949|gb|BF325274.1|BF325274
EST:     CTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: CTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
EST: gi|20812482|gb|BQ296960.1|BQ296960
EST:     TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTG                         GACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG
genomic: TAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattc ... gtcatatcagGACTTGTAAATGCATTGAAACTTCTTCAGCCGATCAAAGACAAATATTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGCTGAAACATGGAGCCAATGCTGgtaatgattcattaaatattgattatttccgaattttgcttatggagtaatattccctgatgaattgtcatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG