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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag

Basic information

species Glycine max
transcript GLYMA02G07910.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag----------
|| |||||||| || || || || |||||||| |||||||||||||| |||||||| || |||||||||| ||| ||||| || || || || |||||| || | ||| | || | || | || ||| | | |||| | | ||| | |||| || |
ATCTTTTGCTGGTGAACTGCTTGAGAAGGCCGAGGAGCTTATCAGGATGGGGTTGCATCCAAGTGAGATCATCATTGGCTACACCAAGGCCATTAATAAGgttacttaccctcccgattga-gctggccttatattgattaaaaaaacctgttgcctgatggcaggctagttattcatgcatttgcatctgcaatgcgcag

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattg-ctgctctctctccctcta-atttcttgttttgttt-cag
|| |||||||| || || || || || ||||| || ||||||||||| ||||||||||| |||||||||| ||| ||||| ||||| ||||||||||| | | || | ||| ||||| | || ||| | ||| | | ||| | || | ||| || | |||
ATCGTTTGCTGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCGAGTGAGATCATCATTGGCTACACCAAAGCCATCAACAAGgtgacacccctccccc-cgactcctgtaggcttctgtacaacattgacatgcagtctgatagcaggtcctttgtgctttgtatttggtatgcag

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgat-ctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag--------------------------
|| ||||| || || || || || || ||||| || ||||||||||| |||||||| || |||||||||| ||| ||||||||||| ||||||||||| || ||| || || || || || ||| || || | | || | | | | || | ||
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgactt-gccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttggtatgcagacaattgagatcttggaggatcttgttgag

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgt-catattgctgctctctctccctctaatttcttgttttgt-ttcag
|| ||||| || || || || || || ||||| || ||||||||||| |||||||| || |||||||||| ||| ||||||||||| ||||||||||| || ||| || || || || | | ||| || || || | | ||| | | ||| | ||| || | |||
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgactt-gccccctgactctggcttttgtaatat----tgaaacgtgcagtctgatag-caggctctttgtgcttttgtctttggtatgcag

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag
|| |||||||| || || || || || ||||| |||||||||||||| | |||||||| |||||||| |||||||| |||||||| ||| ||||||| | | | || | | || | | ||| |||| | | | | | || | || ||
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttgagtatttgacgaatgctattggattttgattatgcag---

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttt--tgatgaaa-gccttagtgatctgtctttaaatgt---catattgctgctctctctccctctaatttcttgttttgt---ttcag
||| |||||||| |||||||| || ||| ||||| |||||||||||||| |||| ||||| |||||||||||||||||| | ||||| || || ||||||| | || || | ||| | ||| | ||||| | ||| || | || | | ||| | | | |||||
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag

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|298170393|gb|HO019017.1|HO019017
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|209718245|gb|BW657850.1|BW657850
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|207795810|gb|GD764077.1|GD764077
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|192299740|gb|FG987785.1|FG987785
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAGATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|209700023|gb|BW656204.1|BW656204
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|16997151|gb|BM086523.1|BM086523
EST:     CAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
genomic: CAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|209728113|gb|BW655348.1|BW655348
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|209721609|gb|BW671736.1|BW671736
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|26045600|gb|CA783137.1|CA783137
EST:     GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
genomic: GTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT
EST: gi|298187418|gb|HO034567.1|HO034567
EST:     ACACTAAAGCAATCAACAAG                         ACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGAGAATATGGAT
genomic: ACACTAAAGCAATCAACAAGgttttttcag ... tttgtttcagACTGTTCAAATATTGGATGAACTAGTTGAGGATGGTTCTGACAATATGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgtcatattgctgctctctctccctctaatttcttgttttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA