RetrogeneDB ID: retro_mmus_2408

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:145632549..145633247(+)
• Located in intron of: ENSMUSG00000097661

Retrocopy information

• Ensembl ID: ENSMUSG00000083562
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cdv3
• Ensembl ID: ENSMUSG00000032803
• Aliases: Cdv3, 2510010F10Rik, C230084J24Rik, C79446, TPP36
• Description: carnitine deficiency-associated gene expressed in ventricle 3 [Source:MGI Symbol;Acc:MGI:2448759]

Sequence

>retro_mmus_2408
GGGACAAGAAGAAGAAGGAATGGAGCAGTCGGGCGGCCAATGCGGCGAGCAGCATGGACGGGAGCAGCGCGTCCGGAGGG
CTCCAAGACGGGTGATGGCGGGAGCTCGGGCTCTGGTGCTAGGACAGGAGACAGCAGGAGCGCGGGCCCTGCTGGCAAGG
ATATAATGAAGGATGAAAATGAGTGGAAAGAATTTGAGCAAAGAGAGGTTGATTACAGTGGATTAAGAGTTCAGGCAATG
CAAATAAGTGAAAAGGAAGAAGATGATAATGAGAAGAGAGAAGATCCATCTCTCTTTGGAAGAAGGTGGAGGTGGCAATG
GAGCAGAAAAATCTTCAGGTCCCTGGAATAAAACCGTTCCGGTACAGGCGCTTCCTTGCTCCAGTAACAGTTACAGAAAC
CCCGGAGCCAGCAATGCCCAGTGGTGTATTTAGGCCTCCTGGGGCAAGGCTAACCACAACAAGGAAAACACCACAAGGAC
CACCAGAAATACACAGTGACACACAGTTCCCATCCCTGCACTCCACTGCCAAGCATGTAGAGAGCCGGAAGGATAAAGAA
ATGGAGAAGAGCTTTGAAGTAGTAAGACACAAAAATAGAGACAGGGAGGATGTTTCAAAAAACCAGGCCCTTAAACTTCA
GCTAGACAACCAGTATGCTGTGCTTGAAAATCAGAAGTACAGCCACACACAGTACAGC

Alignment

ORF - retro_mmus_2408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 80.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GARSGDGGSLGSGSRSG--DGGSSGSGARSGDGGSS----RSGDGGSAGPAGKAITKDENEWKEFEQREV
          G.R....G..G...R.....G.....G...GDGGSS....R.GD..SAGPAGK.I.KDENEWKEFEQREV
Retrocopy GTRRRRNGAVGRPMRRAAWTGAARPEGSKTGDGGSSGSGARTGDSRSAGPAGKDIMKDENEWKEFEQREV

Parental  DYSGLRVQAMQISEKEDDDNEKREDPGD-NWEEGGGGSGAEKSSGPWNKTAPVQAPP-APVTVTETPEPA
          DYSGLRVQAMQISEKE..D............EEGGGG.GAEKSSGPWNKT.PVQA.P.APVTVTETPEPA
Retrocopy DYSGLRVQAMQISEKE-EDDNEKREDPS>SLEEGGGGNGAEKSSGPWNKTVPVQALP>APVTVTETPEPA

Parental  MPSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRDREEVSKN
          MPSGV.RPPGARLTTTRKTPQGPPEI.SDTQFPSL.STAKHVESRKDKEMEKSFEVVRHKNRDRE.VSKN
Retrocopy MPSGVFRPPGARLTTTRKTPQGPPEIHSDTQFPSLHSTAKHVESRKDKEMEKSFEVVRHKNRDREDVSKN

Parental  QALKLQLDNQYAVLENQKYSHTQYS
          QALKLQLDNQYAVLENQKYSHTQYS
Retrocopy QALKLQLDNQYAVLENQKYSHTQYS

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	0.00 RPM	40.39 RPM
SRP007412_cerebellum	0.04 RPM	30.48 RPM
SRP007412_heart	0.00 RPM	46.13 RPM
SRP007412_kidney	0.04 RPM	41.35 RPM
SRP007412_liver	0.03 RPM	51.23 RPM
SRP007412_testis	0.27 RPM	116.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2408 was not detected

EST

No EST(s) were mapped for retro_mmus_2408 retrocopy.

TSS

No TSS is located nearby retro_mmus_2408 retrocopy 5' end.

Lab

retro_mmus_2408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408 , retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,