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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttctgagatttactaaacttgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT

Basic information

species Glycine max
transcript GLYMA13G16170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 3
gtatttttctgagatttactaaacttgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattac--ctctgccaaacttggttttatcttg---gcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
||| | | | | | | | | | || | |||| | | ||||| || || | | | || | | || | | ||| | ||||||||||| |||||||| || || |||||||||||| |||| || |||||||||||||| || || || | | | | || ||||| |||| | |||
------------------gtaacatatctcgcggtcgcggt---tcctagtggaaatgcggttaccttgggacttgcttgaagcgcggagggttttgatatagatgttctgcctttgcgtgtagGCGTGTGCTGATTTTCCCTAAGGGGAACAATGTGGACCATTTCTCTATGTATTTGGATGTCGCGGACTCGGTGAATCTCCCTTATGGATGGAACCGGTAT

upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G551402_T01 (Zea mays), 3'ss of exon 1
gtatttttctgagatttactaaact-tgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
|| | || | || | | || | | | | ||| || || | || | | ||| | | || || |||| | ||| | ||||| ||||||| |||||||| || || |||||||||||| | || || ||||| |||||||||||||| ||| |||| | || ||||||||||| | |||
gtgagctccttatccttccactgttctgcctgcagaaaccatggagttttttccctagcccctc-----tgttctttagagtactcataacatctgttgaccttcat---------gcagGAGTGTGCTGATTTTCCCCAAGGGGAACAATGTGGACCACTTCTCAATGTACTTGGATGTTGCTGACTCAACCAGCCTTCCGTATGGTTGGAGCCGCTAT

upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G426486_T01 (Zea mays), 3'ss of exon 4
gtatttttctgagatttactaaacttgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
| || | | | || | || || | | || ||| | ||| || ||| | || | || | | | || |||| | ||||||||||||| |||||||| || || ||||||||||| | || || |||||||||||||||| ||||| | || | || ||||| ||||| | |||
----------gtgaccttttggatcccttgccactg-tgaccg--ctactggaa---------gcatgggtagatgtctggagagttttaatg-gacgtgctactttttgctt--gcagGCGTGTGCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTATCGTTGTATTTGGATGTTGCGGATTCTGGGAGCCTCCCATATGGGTGGAGCCGGTAT

upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 3
gtatttttctgagatttactaaacttgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
| | ||| || | | | | | | | | | | | | | || ||| | || | |||| |||| ||||||||| || |||||||| || || ||||||||||| | || || ||||||||||||||||| ||||| | | | || || || ||||| | |||
------------------gtgagctt-ttggatctcttctcttgccactgtaactgctgacggaaacatgggtaaatgtttggtgggttttaatggatgtgctactttttgcttg-cagGCGTGTCCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTCTCGATGTATTTGGATGTTGCAGATTCTGGGAACCTCCCATACGGGTGGAGCCGGTAT

upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 3
------------gtatttttctgagatt-tactaaacttgttagtaatggtgttct-attttcttgaatat----gctctggtatgtatacttgttttcagtgatt--acctctgccaaacttggt--tttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
| || || | || | || || ||| || | | | || ||| | | ||| | | | || |||| || | | || | |||||| | | | || || | |||||| ||||||||||| ||||| ||||||||||| || ||||||| ||||| ||||||||||| |||||| | |||||||||||||| ||||||||||||
gtattttaattttttttcatccaaaatggcattattgttattattattatcatcatcatcttcattattattattgttgttgttgctataaccattattcttcatatggctagtgccaatcctcataattgatttgaacagGCGGGTGCTTATTTTTCCAAAGGGAAACAATGTTGAACATTTGTCTATGTACTTGGATGTTGCGGATTCATCAAGTTTGCCCTATGGGTGGAGTAGATAT

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|254314169|gb|GR831798.1|GR831798
EST:     GTTGTTGGTGGCTATAAATG                         GCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA
genomic: GTTGTTGGTGGCTATAAATGgtatttttct ... atcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA
EST: gi|213594478|gb|DB973663.1|DB973663
EST:     AATACAAAGAAGCTCTATTCGGAAATATTTGTTGTTGGTGGCTATAAATG                         GCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA
genomic: AATACAAAGAAGCTCTATTCGGAAATATTTGTTGTTGGTGGCTATAAATGgtatttttct ... atcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA
EST: gi|209699335|gb|BW664054.1|BW664054
EST:     AATACAAAGAAGCTCTATTCGGAAATATTTGTTGTTGGTGGCTATAAATG                         GCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA
genomic: AATACAAAGAAGCTCTATTCGGAAATATTTGTTGTTGGTGGCTATAAATGgtatttttct ... atcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT
                                         ttttatctt  CT-rich tract
 ttttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttctgagatttactaaacttgttagtaatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgattacctctgccaaacttggttttatcttggcagGCGTGTGCTTATTTTCCCAAAAGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCTGATTCAGCCAGTTTGCCCTATGGTTGGAGTAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG