RetrogeneDB ID: retro_mmus_1176

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:13902006..13902464(+)
• Located in intron of: ENSMUSG00000084902

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zfand5
• Ensembl ID: ENSMUSG00000024750
• Aliases: None
• Description: zinc finger, AN1-type domain 5 [Source:MGI Symbol;Acc:MGI:1278334]

Sequence

>retro_mmus_1176
ACAGATTCTGCATCTGTACAGAGAGCAGATGCTAGTTTCAACAATTGTGAAGGTGCTGCTGGCAGCACATCTGAAAAATC
AAGAAATGTGCCTGTGGCTGCCTTGCCTGTAACTCAACAAATGACAGAAATGAGCATTTCATGAGAGGACAAATTAACTA
TCCCGAAAACAGAGGTGTCAGAGTCAGTTGTCACTCAGCTCAGTCCATCAGTTTCTCAGCCCAGTTCTTCTCAAAGTGAA
GAAAAAGCTCCTGAGTTGCCCAAACCAAAGAAGAACAGATGTTCTATTTGTAGAAAGAGAGATGGCCTTACAGGGGTTGA
CTGCCGATGTGGAAATTTGTTTTGTGGACTTCACCATTACTCTGACAAGCACAACTGGCCATATGATTATAAGCAGAAGC
TGCAGCAAAAATCAGAAAAGAAAATCTAGTTGTTGTGGCTCAAAAAATCCAGAGAATA

Alignment

ORF - retro_mmus_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.31 %
• Parental protein coverage: 71.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDSASVQRADAGLNNCEGAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPS
          .DSASVQRADA..NNCEGAAGSTSEKSRNVPVAALPVTQQMTEMSIS.EDK.T.PKTEVSE.VVTQ.SPS
Retrocopy TDSASVQRADASFNNCEGAAGSTSEKSRNVPVAALPVTQQMTEMSIS*EDKLTIPKTEVSESVVTQLSPS

Parental  VSQPSSSQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYK-AEAAAKIR
          VSQPSSSQSEEKAPELPKPKKNRC..CRK..GLTG.DCRCGNLFCGLH.YSDKHN.PYDYK.AEAAAKIR
Retrocopy VSQPSSSQSEEKAPELPKPKKNRCSICRKRDGLTGVDCRCGNLFCGLHHYSDKHNWPYDYK<AEAAAKIR

Parental  KENPVVVAEKIQRI
          KEN.VVVA.KIQRI
Retrocopy KENLVVVAQKIQRI

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	0.02 RPM	97.68 RPM
SRP007412_cerebellum	0.00 RPM	72.04 RPM
SRP007412_heart	0.03 RPM	65.50 RPM
SRP007412_kidney	0.00 RPM	45.91 RPM
SRP007412_liver	0.00 RPM	26.08 RPM
SRP007412_testis	0.00 RPM	19.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1176 was not detected

EST

No EST(s) were mapped for retro_mmus_1176 retrocopy.

TSS

No TSS is located nearby retro_mmus_1176 retrocopy 5' end.

Lab

retro_mmus_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176 ,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,