RetrogeneDB ID: retro_mmus_2878

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:132069332..132069783(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk4
• Ensembl ID: ENSMUSG00000006728
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:MGI Symbol;Acc:MGI:88357]

Sequence

>retro_mmus_2878
AAGCCAGAGAACATTCTCCTGACAATTAATGGGACAGCCAAGCTGGCTGACTTTGTCCTATGCAATATCTATAGCTCTCA
AATGAACAGCATGCCTGTGGTTGTTATGTTCATTGACTGGGCTCCTGAAATTCTTCTTCAGGCTACATGTGTAAGACATG
TGGACACGTGTTGTGTTGGCTGTATCTACTCAGAGATGTTTTGTTGTATGCTTCACTTCCGTGGAAAATCTGAGTCTGAC
AAATTGTGCAAAAATCTTTGATCTCATTGGATTGCCTTCAGAGGATGACTGGCCTCAAGAGATATAGCTAACTGGAAAAG
CACTTGCACCCAGAGGGCCACTCCAGTCAGTGGTTCAAGGAATGGAAGAATCTGGAGCACAGCTGCTTAAGAAAATGCTG
ACCTTTAACCCACATCAGCTAATCTCTGCCTTTTGAGACCTGCAACACTCT

Alignment

ORF - retro_mmus_2878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.4 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPENILVTSNGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRK
          KPENIL.T.NGT.KLADF.L..IYS.QM...PVVV.....APE.LLQ.T....VD...VGCI..EMF...
Retrocopy KPENILLTINGTAKLADFVLCNIYSSQMNSMPVVVMFIDWAPEILLQATCVRHVDTCCVGCIYSEMFCCM

Parental  PLFCGNSEADQL-GKIFDLIGLPPEDDWPREVSLPRGAFAPRGPRPVQSVVPEMEESGAQLLLEMLTFNP
          ..F.G.SE.D.L..KIFDLIGLP.EDDWP.E..L...A.APRGP...QSVV..MEESGAQLL..MLTFNP
Retrocopy LHFRGKSESDKL>AKIFDLIGLPSEDDWPQEI*LTGKALAPRGP--LQSVVQGMEESGAQLLKKMLTFNP

Parental  HKRISAFRALQHS
          H..ISAF..LQHS
Retrocopy HQLISAF*DLQHS

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	26.35 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	26.06 RPM
SRP007412_kidney	0.00 RPM	35.73 RPM
SRP007412_liver	0.00 RPM	21.57 RPM
SRP007412_testis	0.00 RPM	15.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2878 was not detected

EST

No EST(s) were mapped for retro_mmus_2878 retrocopy.

TSS

No TSS is located nearby retro_mmus_2878 retrocopy 5' end.

Lab

retro_mmus_2878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878 , retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,