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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA

Basic information

species Glycine max
transcript GLYMA16G32990.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 1
gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA
                                    ||  | |||   |    ||| | |||||  |    |  ||  | | | |  |     || |  ||  ||||       || ||  |||| |  ||          ||    ||||||| ||||| ||||| ||| |  | ||  | || ||||| || ||  |||||||| | ||||||||||| |||||||||||||| || || ||  |||| |
---------------------------------aaatgaaatatttgctatggaatgacaattttacttaatgctagcacttggttgtttctttgct--tgatgaaa-------cattggatgatgtgctt----------ttcccctgcagGATAATGTCTTTGTTCAGCTTATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAA

upper sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA
                         |||  ||  | ||| | | |  |   | || ||   |||| |     | |  || ||  || | ||  |   | ||  ||||       |||| |  ||| |  ||          ||  | ||||||| ||||| || || ||  || | ||  | || || ||||| ||  | |||||||| || ||||||||||||||||||||||| || || ||| |||| |
-------------------------tctagttcctctgtaataat--gaagtgaaacaccctttgcc-----catgctactcattgcttgtttt---cttgttgaaa-------cagttaacgatatcatt----------tttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA

upper sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 1
gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA
                                ||| |    |||  |  | |   ||| ||  | | || |   |  |||   || |   ||    |||      |||||| ||    |  | ||  |||||          |||| ||||||||||||| ||||| ||  |||| || || || ||||| || |||||||| ||||| || |||||||| || |||||||| || |||||  | |||||||
------------------------------agattcttgtgcatatttatatagttcaaaa--tattagttgtcttgtaaagcattagattgcctttca------aaagaacag----gtataatgatttta----------tgttctgcagGACAATGTATTTGTTCAAATGCTTTGCTCAATCCAATATCGTGTGATTAAAGAAAATGCGGATGATGCCTTTTATGAGTTACAGAACCCCAAAGAGCAGA

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|298190343|gb|HO032464.1|HO032464
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCTGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|254327495|gb|GR837050.1|GR837050
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|213603197|gb|DB960460.1|DB960460
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|254346709|gb|GR856431.1|GR856431
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|192328203|gb|FK022882.1|FK022882
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|298179574|gb|HO028045.1|HO028045
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|209701321|gb|BW655916.1|BW655916
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|298184948|gb|HO030161.1|HO030161
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCCAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|298164789|gb|HO010786.1|HO010786
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCGGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|16347781|gb|BI973376.1|BI973376
EST:     TCTCCTTTATGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|298197264|gb|HO042007.1|HO042007
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
EST: gi|193325061|gb|FK290597.1|FK290597
EST:     CTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCTAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAA
genomic: CTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACC-AAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAA
EST: gi|120530546|gb|EH258679.1|EH258679
EST:     TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAG                         GACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG
genomic: TCTCCACCAGGATCTCCTCCCTCGATGTCCGCATCGAAACCAAAACCAAGgtatttcaat ... tgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA
                                            ttgtttt  CT-rich tract
                        tgatttttttaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG