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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG

Basic information

species Glycine max
transcript GLYMA02G10060.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtactta----taaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
         |    |||||||| |  | ||  | |  |||||    |||| | | ||  ||||  ||  | | |     ||||| |        |    | ||||||||||||||||||| ||||| || || || |||||||| ||||| || || |||||||| || || |||||  ||
---------gtaaactagttat-agttagttctgt--ctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 4
tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
     | |   | | ||  |     ||||| || |          | |||||  ||        |  |  |  |||| |         |  |   | |||||||||| || ||||| ||||| || ||||| ||||||||||| || ||||| ||||| || ||||| || ||  ||
---gtaaatcacttgtaacttgtttcttgttatttgaggggatgatgaaata-gatccttgtttcagctaaactatagaaaaa-----tggcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACTTACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATACTTTCAG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------tatacacaaggcgtctagttatgaactt------gtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattt--------tcccttttactgttt--cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
                                                 |     |||  |  |  ||| ||  |        ||||  |    | || | ||  | || |||   |  ||   |   |  |||||           |||||  ||  |  ||||| | ||||| ||| | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| || ||||| |||
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
----tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgttt-cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG------------
     | |     |   ||||      |  | ||  | |    |||  ||  |  |||   || | ||     |   | |    |    || ||    ||| |||||  |||||||||||||||| | ||||| |||||||| || || || ||||||||||||||||| || |||||  ||            
tcttgaaatttctgaaatctatcagaaaggtagt--tttcatcttggggtttaccatatactgtataga---atctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 5
----tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgttt-cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
     | |     |   |||| | |  ||  || | | |    |||  ||  |  | |   || | ||     |     |    |    || ||    ||| |||||  |||||||||||||||| | ||||| |||||||| || || || ||||||||||||||||| || |||||  ||
tcttgaaatttctgaaatcta-tcagaaaggtg-gttttcatcttggggtttaccaaatactgtataga---atctgcgtgggctaaatctattgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATGTATTTTCAG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 4
----tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgttt-cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
     | |     |   ||||  |  |||     | | |    |||| ||  |  |||   || |  |     |     |    |    || ||    ||| |||||| |||||||||||||||| | ||||| |||||||| || || || ||||||||||||||||| || |||||  ||
ccttaaaatttctgaaatcta--tcagaaaggaggttgtcatcttgaggtttaccatatactgtatgga---atctccgtgggctaaatctgttgaaatttgcagGTGATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG

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|298182211|gb|HO026386.1|HO026386
EST:     GGGTCTAGCACGCCATTTATTTG                         GTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT
genomic: GGGTCTAGCACGCCATTTATTTGgtattcccaa ... actgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT
EST: gi|19053701|gb|BM732368.1|BM732368
EST:     AGCAACAGACTTAAAGCAATGCCTTGAGGGTCTAGCACGTCATTTATTTG                         GTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT
genomic: AGCAACAGACTTAAAGCAATGCCTTGAGGGTCTAGCACGCCATTTATTTGgtattcccaa ... actgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT
EST: gi|22522222|gb|BU081033.1|BU081033
EST:     AGCAACAGACTTAAAGCAATGCCTTGAGGGTCTAGCACGCCATTTATTTG                         GTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT
genomic: AGCAACAGACTTAAAGCAATGCCTTGAGGGTCTAGCACGCCATTTATTTGgtattcccaa ... actgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatataatttgcaaagctacgtacttataaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
                                  ttttcccttttactgt  CT-rich tract
                        tacttataaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG

-atacaca
- - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - - -aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaag