RetrogeneDB ID: retro_mmus_1412

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:81674257..81674714(-)
• Located in intron of: ENSMUSG00000022394

Retrocopy information

• Ensembl ID: ENSMUSG00000092325
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tm2d1
• Ensembl ID: ENSMUSG00000028563
• Aliases: Tm2d1, 2310026L18Rik, AA990549, Bbp
• Description: TM2 domain containing 1 [Source:MGI Symbol;Acc:MGI:2137022]

Sequence

>retro_mmus_1412
TATTTGTAAAAAGAACCAAAAATAAATGATGCTACGCAAGAACCAGTTAATTGTACAAACTACACAGCTCATGTTCAATG
TTTTCCAGCACCCAAAATAACTTATAAAGGATTTGAGTGGTAATGAAACACATTTTACTGGAAGTGAAGTCGGTTTTCTC
AAGCCCATAACTTGCCGAAATGTGAATGGCTATTCGTACAAAGTGGCAGTTGCATTATCTCTCTTTTTGGGATGGCTGGG
AGCAGATCGATTTTACCTCGGATATCCTGCCTTACGCTTGTTAAATTTTTGCACCGTAGGATTTTGCGGAATTGGGAGCC
TAATTGATTTCATTCTTATTTCAATGCAGATTGTTGGACCTTCAGATGGAAGTAGTTACATTATAGACTATTATGGAACC
AGGCTTACAAGACTCAGCATTACTAATGAAACATTTAGAAAAACCTAGCTGTACCCA

Alignment

ORF - retro_mmus_1412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.77 %
• Parental protein coverage: 73.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YICKEPKINDATQEPVNCTNYTAHVQCFPAPKIT-CKDLSGNETHFTGSEVGFLKPISCRNVNGYSYKVA
          Y..KEPKINDATQEPVNCTNYTAHVQCFPAPKIT..KDLSGNETHFTGSEVGFLKPI.CRNVNGYSYKVA
Retrocopy YL*KEPKINDATQEPVNCTNYTAHVQCFPAPKIT>IKDLSGNETHFTGSEVGFLKPITCRNVNGYSYKVA

Parental  VALSLFLGWLGADRFYLGYPALGLLKFCTVGFCGIGSLIDFILISMQIVGPSDGSSYIIDYYGTRLTRLS
          VALSLFLGWLGADRFYLGYPAL.LL.FCTVGFCGIGSLIDFILISMQIVGPSDGSSYIIDYYGTRLTRLS
Retrocopy VALSLFLGWLGADRFYLGYPALRLLNFCTVGFCGIGSLIDFILISMQIVGPSDGSSYIIDYYGTRLTRLS

Parental  ITNETFRKTQLYP
          ITNETFRKT.LYP
Retrocopy ITNETFRKT*LYP

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	0.26 RPM	9.63 RPM
SRP007412_cerebellum	0.22 RPM	10.20 RPM
SRP007412_heart	0.16 RPM	14.10 RPM
SRP007412_kidney	0.19 RPM	19.54 RPM
SRP007412_liver	0.03 RPM	8.71 RPM
SRP007412_testis	0.09 RPM	4.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1412 was not detected

EST

No EST(s) were mapped for retro_mmus_1412 retrocopy.

TSS

No TSS is located nearby retro_mmus_1412 retrocopy 5' end.

Lab

retro_mmus_1412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1412 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412 , retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,