RetrogeneDB ID: retro_mmus_3073

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:104692300..104693315(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rrm2
• Ensembl ID: ENSMUSG00000020649
• Aliases: Rrm2, AA407299, R2
• Description: ribonucleotide reductase M2 [Source:MGI Symbol;Acc:MGI:98181]

Sequence

>retro_mmus_3073
AGGAGAATGTTCCGGGACTCCAGGGAGCTGGAAAGTAAAGTGCCTACTAACCCCAGCCTTGAGGGTGAGCCATTACTGAG
AGAAAATCCCTGCCATTTTGTTGTCTTTCCCATTGAATACTATGATATCTGGCAGATGTACAAGAAAGCTGAGGCCTCCT
TTTGGACTGCCAAGGAGGTGGACCTTTCCAAGGGTATTCAACACTGGGAAGCTCTGAAACTGGATGAGAGATATTTTATA
GCTCACGTTCTGGCTTTCTTTGTAGCGAGTGATGGCATAGTCAATGAAAACTTGGTGGAGCGATTTAGCCAAGAAGTTCA
AGTTACAGAGGCCCGCTGTTTCTATGGCTTCTAAATTGCCATGGAAAACATACACTCTGAAATGTACAGTCCCCTTATTG
ACACTTACATTAAAGATTCCAAGGAAAGAGAATATCTCTTCAATGCTATTTAAACAATGCCTTGTGTGAAGAAGAAGGCT
GACTGGGCCTTGCGTTGGACTGGGGACAAAGAGTCCCCATATGGAGAATGAGTTGTGGCCTTTGCTGTGGTGGAAGGAGT
CTTCTTTGCATCGATATTCTGGCTCAAGAATCGCAGACTGATGCCGGGTCTTACACTTTCCAATGAGCTTATTAGCAGAG
ACAAGGGTTTACACTGGGACTCTGCCTGCCTGATGTTCAAGCACCTGGTACACAAGCCATTGGAGCAAAGAGTAAAAGAT
ATAAAACACCAACACTGTTAGGATAGGGCAGGAGTTTCTCATGGAGGCTTTGCCTGTGAAGCTCTTCGGGGCAAATTGCA
CTTTGATGAAGCAGTACATTGAATTTTTGGCTGACAGGCTTCCACTGGAGCTGGGTGTTAAGAAGATTTTCAGAGTAGAA
AATCCATTTGACTTCACGGAAAATATTTCACTAGAAGGAAAAACAGACTTCTTTGAGAAGCAAGTAGGCGAGTATCAGAG
GATGGGAGTCATGTCGAATTCCACAGAGAATTCTTTTACCTTGCATGCTGACTTC

Alignment

ORF - retro_mmus_3073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 87.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRIFQDSAELESKAPTNPSVEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWE
          RR.F.DS.ELESK.PTNPS.E.EPLLRENP..FVVFPIEY.DIWQMYKKAEASFWTA.EVDLSK.IQHWE
Retrocopy RRMFRDSRELESKVPTNPSLEGEPLLRENPCHFVVFPIEYYDIWQMYKKAEASFWTAKEVDLSKGIQHWE

Parental  ALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDP
          ALK.DER.FI.HVLAFF.ASDGIVNENLVERFSQEVQVTEARCFYGF.IAMENIHSEMYS.LIDTYIKD.
Retrocopy ALKLDERYFIAHVLAFFVASDGIVNENLVERFSQEVQVTEARCFYGF*IAMENIHSEMYSPLIDTYIKDS

Parental  KEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTF
          KEREYLFNAI.TMPCVKKKADWALRW.GDKE..YGE.VVAFA.VEG.FF....ASIFWLK.R.LMPGLT.
Retrocopy KEREYLFNAI*TMPCVKKKADWALRWTGDKESPYGE*VVAFAVVEGVFF----ASIFWLKNRRLMPGLTL

Parental  SNELISRDEGLHCDFACLMFKHLVHKPAEQRVREI-ITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEF
          SNELISRD.GLH.D.ACLMFKHLVHKP.EQRV..I..TN.VRI.QEFL.EALPVKL.G.NCTLMKQYIEF
Retrocopy SNELISRDKGLHWDSACLMFKHLVHKPLEQRVKDI>NTNTVRIGQEFLMEALPVKLFGANCTLMKQYIEF

Parental  VADRLMLELGFNKIFRVENPFDFMENISLEGKTNFFEKRVGEYQRMGVMSNSTENSFTLDADF
          .ADRL.LELG..KIFRVENPFDF.ENISLEGKT.FFEK.VGEYQRMGVMSNSTENSFTL.ADF
Retrocopy LADRLPLELGVKKIFRVENPFDFTENISLEGKTDFFEKQVGEYQRMGVMSNSTENSFTLHADF

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	1.17 RPM
SRP007412_cerebellum	0.00 RPM	0.91 RPM
SRP007412_heart	0.00 RPM	1.62 RPM
SRP007412_kidney	0.00 RPM	3.00 RPM
SRP007412_liver	0.00 RPM	3.74 RPM
SRP007412_testis	0.00 RPM	10.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3073 was not detected

EST

No EST(s) were mapped for retro_mmus_3073 retrocopy.

TSS

No TSS is located nearby retro_mmus_3073 retrocopy 5' end.

Lab

retro_mmus_3073 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3073 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073 ,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,