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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT

Basic information

species Glycine max
transcript GLYMA07G03680.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03680.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g05080.1 (Oryza sativa), 3'ss of exon 4
-------------gtatcagaatattccttgtttct----cttaatg--tcttcttgcatgtgaacttcttcccaaggtg----atgaaaaaagctagaatt-ctggttatggtgttta-tgagggggtgaacaacttgttttgat---tacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
             | ||   ||| |||||||||| |      ||| |   ||||| | |||  | ||||| |   |  |     || || |    | || |  |     ||||  || | | |    |  ||   |     |||||   | ||||||| ||||||||||| || ||||||||| ||||||||| |||||| |||||||| || || ||| | ||||||||    
gtatagtacctgtgcatgctaat-ttccttgtttttgacctataaagaagcttctaggatgaaatcttctcctgcatcttctctataaatattcatcgactaaccaccaatggaattaacttaaactgcaaattgcaatgattgatattttcagAGGACGAGCATGATGTCGTGTGGTTTTGGTTGGAGAAAGGCAAGCCACATGAATGCCCTGTCTGCACTCAGTATTTCTCG

upper sequence: GLYMA07G03680.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
gtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
                    ||  | | |||   ||||  |   | |     | | |       ||| |   |  ||| |||||       ||| |             |||| |||   ||||||||||||||||||||||||| ||||| ||| || | |||||  | || ||||| || ||||| ||  |||| |||||||| 
-------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG

upper sequence: GLYMA07G03680.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06000.t01 (Vitis vinifera), 3'ss of exon 4
gtatcagaatattccttgtttctcttaat-gtcttcttgcatgtga--acttcttccca--aggtgat--gaaaaaagctagaattctggttatggtgttta-tgagggggtgaacaacttgtttt--gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
|||      | |  |||  |    |||||  |  | || ||| |    | ||||| | |  |  | ||  | |      || | |  |  | ||  || ||  |  |    | |   | |||||||  |  | |||||||||||||||||||||||||||||||||||||||||| |||| | |||||||| || |||||| ||||||||||    
gtaagcctctgtcacttactctctttaattattattttccatttatttatttcttacaattaattaatttgcatcccattaaattctttctaattttggttgctctgttatttatttatttgtttttcgtctgcagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCACATGAATGCCCTGTGTGCTCACAGTATTTCACG

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|14126582|gb|BG791020.1|BG791020
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGA-G-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|15812956|gb|BI785231.1|BI785231
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|120496663|gb|EH224830.1|EH224830
EST:     TTACTATGATAAAAGGATAGTCGGATGCCCATGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGATATTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|31306843|gb|CD392046.1|CD392046
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|192330937|gb|FK023110.1|FK023110
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCCGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|120496630|gb|EH224797.1|EH224797
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|193557652|gb|FK511965.1|FK511965
EST:     GGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: GGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|37997246|gb|CF808835.1|CF808835
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|31308540|gb|CD393743.1|CD393743
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|31476276|gb|CD418304.1|CD418304
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
EST: gi|58024911|gb|CX711652.1|CX711652
EST:     TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGT-GAG-                         GATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA
genomic: TCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGGTGAgtatcagaat ... gattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
                                         ttttgat  putative branch site (score: 4)
                                         ttttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA