RetrogeneDB ID: retro_mmus_2646

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:34306717..34307176(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ormdl2
• Ensembl ID: ENSMUSG00000025353
• Aliases: Ormdl2, 0610012C09Rik
• Description: ORM1-like 2 (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914094]

Sequence

>retro_mmus_2646
ATGAATGTGGGGGTGGCACACAGCGAAGTAAACCCCAACACTCTAGTGATGAACAGTTTGGGCATCTGGCTGGCCTACAT
CATCTCGGTAGGACTGCTGCACGTGGTTCTCCTCAGCATCCCTTTCTTCAGCATTCCTGTTATCTGGACCCTGACCAACG
TCATCCATAACTTGGCAATGTATATCTTCCCACATACAGTCAAAGGGACGCCCTTTGAGACCCCTGACCAAGGAAAGGGT
CAGCTTTTGACACATTGGGGGCAGATGGACTATGGACTACAGTTTACCTCCTCACGAAAGTTCCTCAGCATCTCTCCTAT
TATACTCTACCTCCTGGCCAGCTTCTACACCAAGTGTGATGCTGCTCACTTCCTCATCAACACTGCCTCACTGCTCAGCA
TGCTGCTGCCTAAGCTACCCCAGTTCCATGGGGTTCATCTCTTTGGAATCAACAAATAC

Alignment

ORF - retro_mmus_2646 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNVGVAHSEVNPNTRVMNSRGIWLAYIILVGLLHVVLLSIPFFSIPVVWTLTNVIHNLAMYIFLHTVKGT
          MNVGVAHSEVNPNT.VMNS.GIWLAYII.VGLLHVVLLSIPFFSIPV.WTLTNVIHNLAMYIF.HTVKGT
Retrocopy MNVGVAHSEVNPNTLVMNSLGIWLAYIISVGLLHVVLLSIPFFSIPVIWTLTNVIHNLAMYIFPHTVKGT

Parental  PFETPDQGKARLLTHWEQMDYGLQFTSSRKFLSISPIVLYLLASFYTKYDAAHFLINTASLLSVLLPKLP
          PFETPDQGK..LLTHW.QMDYGLQFTSSRKFLSISPI.LYLLASFYTK.DAAHFLINTASLLS.LLPKLP
Retrocopy PFETPDQGKGQLLTHWGQMDYGLQFTSSRKFLSISPIILYLLASFYTKCDAAHFLINTASLLSMLLPKLP

Parental  QFHGVRLFGINKY
          QFHGV.LFGINKY
Retrocopy QFHGVHLFGINKY

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	0.07 RPM	2.43 RPM
SRP007412_cerebellum	0.09 RPM	4.39 RPM
SRP007412_heart	0.00 RPM	1.87 RPM
SRP007412_kidney	0.06 RPM	14.48 RPM
SRP007412_liver	0.11 RPM	19.06 RPM
SRP007412_testis	0.18 RPM	16.37 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2646 was not detected

EST

No EST(s) were mapped for retro_mmus_2646 retrocopy.

TSS

No TSS is located nearby retro_mmus_2646 retrocopy 5' end.

Lab

retro_mmus_2646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003047	2 retrocopies	retro_amel_140, retro_amel_735,
Canis familiaris	ENSCAFG00000000071	8 retrocopies	retro_cfam_1078, retro_cfam_1248, retro_cfam_1512, retro_cfam_1786, retro_cfam_187, retro_cfam_335, retro_cfam_576, retro_cfam_972,
Choloepus hoffmanni	ENSCHOG00000009601	1 retrocopy	retro_chof_2232,
Erinaceus europaeus	ENSEEUG00000015224	1 retrocopy	retro_eeur_16,
Felis catus	ENSFCAG00000013964	1 retrocopy	retro_fcat_895,
Macropus eugenii	ENSMEUG00000014896	1 retrocopy	retro_meug_767,
Microcebus murinus	ENSMICG00000010920	1 retrocopy	retro_mmur_212,
Myotis lucifugus	ENSMLUG00000003575	1 retrocopy	retro_mluc_901,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Mustela putorius furo	ENSMPUG00000000911	2 retrocopies	retro_mputfur_452, retro_mputfur_738,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646 ,
Mus musculus	ENSMUSG00000038150	1 retrocopy	retro_mmus_2464,
Otolemur garnettii	ENSOGAG00000001695	2 retrocopies	retro_ogar_3016, retro_ogar_951,