RetrogeneDB ID: retro_mmus_2220

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:10753892..10754286(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vbp1
• Ensembl ID: ENSMUSG00000031197
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 [Source:MGI Symbol;Acc:MGI:1333804]

Sequence

>retro_mmus_2220
CTCAGAAAGATGGGAAAGGGGCTGAAAGGTCAGATTCCTGAAATTAAACAGACTTTAGAAATTCTGAAATACATGCAAAA
GGAACAAGAGCCCACCAATTCAATGGAGACCAGATTTTTATTGGCAGATAACTTGGACTGCAAAGCTTCAGTGTTCCTAC
TGATAAAGTGTGCCTATGGTTGGGGACTAATGTGATGCCTAAATATATTATTGATGAAGCTCAGGCATTGTTGGAAAAGA
ATTTATCAACTGCTACAAAGAATCTTCATTCTCTTGAGAAAGACCACAACTGTCTTCAAGATCAATTTCACAACTACAGG
CATCAAAATAGCCAGGGTTTATAATCAGGATTAAAAGAGAAAAAAACAAAAGTGTTCCTACCAAGAACAACGCA

Alignment

ORF - retro_mmus_2220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.88 %
• Parental protein coverage: 66.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAQKKRRLKGQIPEIKQTLEILKYMQKKKESTNSMETRFLLADNLYCKASV-PPTDKVCLWLGANVMLEY
          L......LKGQIPEIKQTLEILKYMQK..E.TNSMETRFLLADNL.CKASV..PTDKVCLWLG.NVM..Y
Retrocopy LRKMGKGLKGQIPEIKQTLEILKYMQKEQEPTNSMETRFLLADNLDCKASV<VPTDKVCLWLGTNVMPKY

Parental  DIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQ-FTTTEVNMARVYNWDVKR-RNKDDSTKNKA
          .IDEAQALLEKNLSTATKNL.SLE.D...L.DQ.FTTT....ARVYN.D.KR..NK...TKN.A
Retrocopy IIDEAQALLEKNLSTATKNLHSLEKDHNCLQDQ>FTTTGIKIARVYNQD*KR>KNKSVPTKNNA

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	32.24 RPM
SRP007412_cerebellum	0.00 RPM	36.60 RPM
SRP007412_heart	0.00 RPM	21.57 RPM
SRP007412_kidney	0.00 RPM	23.02 RPM
SRP007412_liver	0.00 RPM	7.97 RPM
SRP007412_testis	0.00 RPM	4.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2220 was not detected

EST

No EST(s) were mapped for retro_mmus_2220 retrocopy.

TSS

No TSS is located nearby retro_mmus_2220 retrocopy 5' end.

Lab

retro_mmus_2220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2220 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220 ,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,