RetrogeneDB ID: retro_mmus_3311

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:121247301..121247573(+)
• Located in intron of: ENSMUSG00000040936

Retrocopy information

• Ensembl ID: ENSMUSG00000091336
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tomm20
• Ensembl ID: ENSMUSG00000093904
• Aliases: Tomm20, 1810060K07Rik, BB284719, Gm19268, MAS20, MOM19, TOM20, mKIAA0016
• Description: translocase of outer mitochondrial membrane 20 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1915202]

Sequence

>retro_mmus_3311
ATGTTGCTGTCTTCATGCATCTACTTCCACCACAAAAGCCAGAGTGGCCCCAACTTTAAGAACAGGCTTCAAGAACGAGG
AAGAACAAGCTTGCTAAGGAGAGCCGGTCTTTCCCAGTTCCCTGACTTAAAAGATGCTGACGCTGTCCAGAACTCTTCCC
TGAAGAGACACAGCTTGGTGAAGAGTTACTACCGCAAGGTGACTACGAGAAGGGTGCAGACCACCTGACAAGCGCAATCG
CCGTGTGCACACAGTCTCAGCAGCCGCTGCAG

Alignment

ORF - retro_mmus_3311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 64.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQ-KFFLEEIQLGEELLAQG
          .....CIYF..K..S.PNFKNRL.ER.....L...RAGLS..PDLKDA.AVQ...F.EE.QLGEELL.QG
Retrocopy MLLSSCIYFHHKSQSGPNFKNRLQERGRTSLL--RRAGLSQFPDLKDADAVQ<ELFPEETQLGEELLPQG

Parental  DYEKGVDHLTNAIAVCGQPQQLLQ
          DYEKG.DHLT.AIAVC.Q.QQ.LQ
Retrocopy DYEKGADHLTSAIAVCTQSQQPLQ

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	273.49 RPM
SRP007412_cerebellum	0.04 RPM	132.87 RPM
SRP007412_heart	0.00 RPM	19.55 RPM
SRP007412_kidney	0.02 RPM	62.31 RPM
SRP007412_liver	0.00 RPM	19.12 RPM
SRP007412_testis	0.00 RPM	19.16 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3311 was not detected

EST

No EST(s) were mapped for retro_mmus_3311 retrocopy.

TSS

No TSS is located nearby retro_mmus_3311 retrocopy 5' end.

Lab

retro_mmus_3311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000562	5 retrocopies	retro_btau_1025, retro_btau_1147, retro_btau_1357, retro_btau_492, retro_btau_533,
Choloepus hoffmanni	ENSCHOG00000002383	7 retrocopies	retro_chof_1381, retro_chof_1699, retro_chof_2252, retro_chof_2497, retro_chof_2511, retro_chof_415, retro_chof_901,
Callithrix jacchus	ENSCJAG00000018127	3 retrocopies	retro_cjac_1860, retro_cjac_2420, retro_cjac_918,
Erinaceus europaeus	ENSEEUG00000000221	1 retrocopy	retro_eeur_544,
Echinops telfairi	ENSETEG00000017693	4 retrocopies	retro_etel_1224, retro_etel_130, retro_etel_1514, retro_etel_559,
Homo sapiens	ENSG00000173726	5 retrocopies	retro_hsap_1827, retro_hsap_1906, retro_hsap_3866, retro_hsap_4702, retro_hsap_796,
Gorilla gorilla	ENSGGOG00000025184	5 retrocopies	retro_ggor_1395, retro_ggor_2166, retro_ggor_2606, retro_ggor_2923, retro_ggor_656,
Loxodonta africana	ENSLAFG00000015499	1 retrocopy	retro_lafr_436,
Microcebus murinus	ENSMICG00000016325	3 retrocopies	retro_mmur_1055, retro_mmur_245, retro_mmur_989,
Myotis lucifugus	ENSMLUG00000016218	1 retrocopy	retro_mluc_644,
Macaca mulatta	ENSMMUG00000007136	2 retrocopies	retro_mmul_1255, retro_mmul_273,
Monodelphis domestica	ENSMODG00000008452	6 retrocopies	retro_mdom_1112, retro_mdom_1172, retro_mdom_1297, retro_mdom_1527, retro_mdom_1568, retro_mdom_838,
Mus musculus	ENSMUSG00000093904	12 retrocopies	retro_mmus_1437, retro_mmus_1669, retro_mmus_1698, retro_mmus_1990, retro_mmus_2026, retro_mmus_2141, retro_mmus_3142, retro_mmus_3311 , retro_mmus_3637, retro_mmus_3655, retro_mmus_457, retro_mmus_935,
Oryctolagus cuniculus	ENSOCUG00000021470	2 retrocopies	retro_ocun_1495, retro_ocun_795,
Otolemur garnettii	ENSOGAG00000032693	2 retrocopies	retro_ogar_3167, retro_ogar_507,
Pongo abelii	ENSPPYG00000000099	4 retrocopies	retro_pabe_1497, retro_pabe_1553, retro_pabe_3650, retro_pabe_708,
Pan troglodytes	ENSPTRG00000002127	5 retrocopies	retro_ptro_1166, retro_ptro_1252, retro_ptro_2634, retro_ptro_3124, retro_ptro_554,
Pteropus vampyrus	ENSPVAG00000015157	1 retrocopy	retro_pvam_346,
Rattus norvegicus	ENSRNOG00000019980	4 retrocopies	retro_rnor_1191, retro_rnor_1958, retro_rnor_1983, retro_rnor_2103,
Sarcophilus harrisii	ENSSHAG00000015876	3 retrocopies	retro_shar_272, retro_shar_512, retro_shar_669,
Ictidomys tridecemlineatus	ENSSTOG00000027564	3 retrocopies	retro_itri_248, retro_itri_71, retro_itri_820,
Tupaia belangeri	ENSTBEG00000003827	26 retrocopies	retro_tbel_1483, retro_tbel_2215, retro_tbel_2239, retro_tbel_2240, retro_tbel_2340, retro_tbel_2348, retro_tbel_2440, retro_tbel_2472, retro_tbel_2548, retro_tbel_2610, retro_tbel_2619, retro_tbel_3000, retro_tbel_3182, retro_tbel_3204, retro_tbel_3674, retro_tbel_3687, retro_tbel_3729, retro_tbel_3808, retro_tbel_3895, retro_tbel_3949, retro_tbel_4068, retro_tbel_4096, retro_tbel_4136, retro_tbel_4596, retro_tbel_4625, retro_tbel_600,
Tursiops truncatus	ENSTTRG00000002200	4 retrocopies	retro_ttru_1114, retro_ttru_183, retro_ttru_870, retro_ttru_982,
Vicugna pacos	ENSVPAG00000003980	1 retrocopy	retro_vpac_252,