RetrogeneDB ID: retro_mmus_3385

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:118571607..118572093(-)
• Located in intron of: ENSMUSG00000038708

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam64a
• Ensembl ID: ENSMUSG00000020808
• Aliases: Fam64a, 2610008F03Rik, 6720460F02Rik, AI115087, CATS
• Description: family with sequence similarity 64, member A [Source:MGI Symbol;Acc:MGI:1924434]

Sequence

>retro_mmus_3385
GGATAGGCCTGGAAAGTCCAGAGCCAGGGCAGCAAGGTCTTCAGGCTGCAGCTCGCTCAGCCAAAAGTGCCTTCCGTGCT
ATGTCCCATAGGATCCAGGAGTCCTGTCAGTGGCACCAAGTGGCTAATGGAGACACAGGTGAAAGTGAGGAGGAAGCCAG
GAGCCCAGAAAGACAGATGGTCGCCACCACCCAGTTTGAGCCAAAAAAACACTTGGCTATGCAGAAACACTAGAATGCTT
CAGAGGGGGACACCCTCGCCTCTCTGGGCAGATGGCTCCACAAGCCCATTGTCATCAGCAGCTAAGGAGAGAGGCTGCCC
TCCAGAGCCCCTGTTCCTCTACAGATCCTCTCTGCTCTCCCAGTGAGTCTGACAGTGACCTAGAGCCTGTGGGAGCTGGA
ATCCAGCATCTTCAGCTGTCTCAAAAGCTGGACAGAGCCATGAAGGCTGAAGAGAGGGTGACATGACCGTCTCCCTTATC
CATGAA

Alignment

ORF - retro_mmus_3385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.08 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPSWKRLESPEPEQQGLQAAARSAKSALGAMSQRIQESCQSGTKWLMETQVKVRRKRGAQKDRGSPPPSL
          G..WK...S.......LQ.A.....S.L.....R...S..SGTKWLMETQVKVRRK.GAQKDR.SPPPSL
Retrocopy G*AWK-VQSQGSKVFRLQLAQPKVPSVLCPIGSR---SPVSGTKWLMETQVKVRRKPGAQKDRWSPPPSL

Parental  SQKNTRLCRANR-DARVGGHLRLSG-QMGPHAHRRQRLRRESALRSPCSSTEPLCSPSESDSDLEPVGAG
          SQKNT.LCR..R..A..G..L...G.QM.P.AH..Q.LRRE.AL.SPCSST.PLCSPSESDSDLEPVGAG
Retrocopy SQKNTWLCRNTR<NASEGDTLASLG<QMAPQAHCHQQLRREAALQSPCSSTDPLCSPSESDSDLEPVGAG

Parental  IQHLQKLSQRLDRAIKAEE-SGDMTVSLIRE
          IQHLQ.LSQ.LDRA.KAEE..GDMTVSLI.E
Retrocopy IQHLQ-LSQKLDRAMKAEE<EGDMTVSLIHE

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	0.12 RPM	0.33 RPM
SRP007412_cerebellum	0.09 RPM	0.30 RPM
SRP007412_heart	0.06 RPM	0.37 RPM
SRP007412_kidney	0.10 RPM	0.25 RPM
SRP007412_liver	0.03 RPM	0.08 RPM
SRP007412_testis	0.00 RPM	0.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3385 was not detected

EST

No EST(s) were mapped for retro_mmus_3385 retrocopy.

TSS

No TSS is located nearby retro_mmus_3385 retrocopy 5' end.

Lab

retro_mmus_3385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385 ,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,