RetrogeneDB ID: retro_mmus_1896

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:24179111..24179929(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ddx6
• Ensembl ID: ENSMUSG00000032097
• Aliases: Ddx6, 1110001P04Rik, E230023J21Rik, HLR2, mRCK/P54, p54, rck
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 [Source:MGI Symbol;Acc:MGI:104976]

Sequence

>retro_mmus_1896
AAGACATTAAAACTCCCTCCAAAGGATCTAAGAATCAAAACTCTGGATGTGACCTCCACAAAAGGAAATGAGTTTGAAGA
TTACTGTTTGAAACGAGAGTTGCTAATAGGAATTTTTGAAATGGGCTGGGAAAAAACCATCTTCTATTCAGGAGGAGAGC
ATTCCCATTGCTTTATCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAAAGCGGTGCCTACCTCATCCC
CTTACTTGAAAGGCTGGACCTGAAGAAGGACAATATTCAAGCAATGGTGATTGTTCCCACTAGAGAACTTGCTCTACAGG
TCAGTCAGATTTGCATCCAGGTCAGCAAACACATGGGAGGGGCCAAAGTGATGGCAACCACAGGAGGAACCAATTTACGG
GATGACGTAATGAGGCTTGATGATACAGGGCATGTGGTGATTGCTACCCCTGGCAGAATCCTGGATCTTATCAAGAAATG
CCTAGAAAAGGTTGATCATGTCCAGATGGTAGTATTGGATGAGGCAGATAAATTGTTGTCACAGGACTTTGTGCAGATAA
TGGAGGCTTTTATTCTCACACTACCTAAAAATAGGCAGATTTTACTATATTCCGCTACTTTCCCTCTTAGTGTACAAAAG
TTTATGAATTCCCATCTGCAAAAACCCTACGAGATAAACCTGATGGAGGAACTAACTCTGAAAGGAGTAACTTAGTACTA
CACATATGTAACAGAGTACAAAAAAAGTGCACTGCCTCAATACACTTTTCTCCAGGCTTCAGATAAACCATCCCATCACT
TTCTGCAACTGTTCTCAG

Alignment

ORF - retro_mmus_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 56.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTLKLPPKDLRIKTSDVTSTKGNEFEDYCLKRELLMGIFEMGWEK-PSPIQEESIPIALSGRDILARAKN
          KTLKLPPKDLRIKT.DVTSTKGNEFEDYCLKRELL.GIFEMGWEK.PS.IQEESIPIALSGRDILARAKN
Retrocopy KTLKLPPKDLRIKTLDVTSTKGNEFEDYCLKRELLIGIFEMGWEK>PSSIQEESIPIALSGRDILARAKN

Parental  GTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL
          GTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDD.MRL
Retrocopy GTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDVMRL

Parental  DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPL
          DDT.HVVIATPGRILDLIKK...KVDHVQM.VLDEADKLLSQDFVQIME..ILTLPKNRQILLYSATFPL
Retrocopy DDTGHVVIATPGRILDLIKKCLEKVDHVQMVVLDEADKLLSQDFVQIMEAFILTLPKNRQILLYSATFPL

Parental  SVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTE-RQKVHCLNTLFSRLQINQSIIFCNSSQ
          SVQKFMNSHLQKPYEINLMEELTLKGVT.YY.YVTE...KVHCLNTLFSRLQIN..I.FCN.SQ
Retrocopy SVQKFMNSHLQKPYEINLMEELTLKGVT*YYTYVTE>TKKVHCLNTLFSRLQINHPITFCNCSQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.05 RPM	176.95 RPM
SRP007412_cerebellum	0.17 RPM	176.46 RPM
SRP007412_heart	0.06 RPM	144.13 RPM
SRP007412_kidney	0.37 RPM	182.01 RPM
SRP007412_liver	0.03 RPM	120.70 RPM
SRP007412_testis	0.09 RPM	69.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1896 was not detected

EST

No EST(s) were mapped for retro_mmus_1896 retrocopy.

TSS

No TSS is located nearby retro_mmus_1896 retrocopy 5' end.

Lab

retro_mmus_1896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1896 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896 ,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,