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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

Basic information

species Glycine max
transcript GLYMA16G23340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
ttttgttaaaaatattcttggc-ctctacacatactatcaccaattgttctttcaa---ttaagagttagttatttaccattttttgaatttgaaatga---gacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
       ||  | ||||    |  |||||| ||| |||| ||  | |  || | ||     ||  ||     | ||||  ||||   | | |  | ||    | |||| ||||||||||| |||||||| ||  | ||||||||||||||||| || || ||||| | ||||
------aaattaaattccaatcattctacagataatatcccct-tcgacctgtaaagatccaactgtagcccacttacatttttcacattgtttattgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
ttttgttaaaaatattcttggcctctacacatactatcaccaattgtt---ctttcaattaagagttagttatt-taccattttttgaatttgaaatga---gacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
       ||  |    | |  | | |||||| ||   | || |  ||    | |    ||   ||      ||  |   || ||   |||    | |     |||||| ||||||||||| |||||||||||  | ||||||||||||||||| || || || || | ||||
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 4
---ttttgtta-aaaatattcttggcctctacacatactatcaccaattgttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
   |  ||  | || || | | ||  | | ||   ||  || |    |     |   |  |     |   |   ||  ||   |    |||| |     | |||| |||||||| || |||||||||||  | ||||||||||||||||| || || || || | ||||
aactagtggcacaacatgtgcgtgaaccc-acgggtagcataaagcctcaggttgcaagctgcacatccttatattttcacaatgcacatttcatt---ggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG

upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 5
ttttgttaaaaatattcttggcct-ctacacatactatcaccaattgttcttt-caattaagagtt--agttatttaccattttttgaatttgaa---atgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
   || | ||     | | ||||| ||       |  ||   |  |  | ||   | ||| |||||     |  |    || |||||  ||| |    ||  | |||| ||||| ||||| || ||||||||||| ||||| ||||| |||||||| ||||| || | ||||
---tgcttaa----ctttcggcctgctgtctgatccgtctagacctacttttaatagttatgagtttcgtctggtgcttatgttttgtgtttcatcatatatgccagATCTTCGGGATGACAAACAGTTCTTCATTGACCACCCTGGCGCTGTACCAATTACTACTGCTCAG

upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaa-gagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
   |||  |  |  |   |  | |    | | ||  |  | |  | |||  |||| | | ||    |   |||   ||| | | |  |||      | |||| ||||||||||| || ||||| ||||| ||||||||||||||||| || |||||||| ||||||
-actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
----ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
     || ||  ||   |||    |  |      |   |||      || || |   |||||| |  |  || |||  |   |||| ||| | || ||||  ||| ||||| || || |||||||||||||||||||||||||||||||| |||||  |  | | ||||
ctaaattagtagaaggaatttgcag--taggagtaggttatttatggtt-ttgtgataattaacaaatt-ttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

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|192330643|gb|FK021962.1|FK021962
EST:     GAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGCACAAAGCTTG                         ACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCA
genomic: GAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGCACAAAGCTTGgtaaattaat ... aatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCA
EST: gi|192330642|gb|FK021961.1|FK021961
EST:     GAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGCACAAAGCTTG                         ACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCA
genomic: GAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGCACAAAGCTTGgtaaattaat ... aatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG
                     ttatttaccatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

- - - -aaaaata
- - - - - - - - - - - - - -cacatac
- - - - - - - - - - - - - - - - - - tcaccaa