RetrogeneDB ID: retro_mmus_1219

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:78703919..78704563(+)
• Located in intron of: ENSMUSG00000034731

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_1219
ATCAAAGTGACCCTAGTGTTTGAGCATACAAACCAGGACAAACAGACATATATGGACAGGGCATACCCAGCAGGCTTGCA
ACTTGAGACGTGAAGGATCTAATGCACTTATTTCAAAGAGGTCCAGATCTCCTTTATAAAAATTGCATAGTACACAGAGA
ACCGAAGCCAGAGAACATTCTAGTGCTGAGTAGTGGGACAGTCAAGCTGGCTGACTTTGACTTAGCCAGAATCTGCAGCT
AACAGATGGCCCTCACACCTGCAGTTGTTACACTCCAGCACCATGCTCCTGGAATTCTTCTGTAGTCTACATATGCAACG
CCTGTGGACCTGTGGAGTGTCGGCTGTATCTCTGCAGAGATGTCTGGACAAAATCCTCTCTCCTATGGACATTCTGAAGA
TGACCAGTTAGACAAAATCTGTGATCAGATTGCCCTGCCTCCAGAGGATCAGTGGCCTGGAAACATCTCTCTCCCCAGAG
CCTTTTTCCCCAAAGAGACTGGGCCAGTCCAGTCCATGGTGACAGAGATGGAGGAGCCTAGAGCACCGTCCATCTGGAAA
TGCTGACCTTTGAAGCACATAAGCAAACCTGCACCACTGAGCCCTGCATCCCTGTGATCTACACAGGAGGACCGTGATGC
AGAG

Alignment

ORF - retro_mmus_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.44 %
• Parental protein coverage: 71.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKVTLVFEHIDQDLRTYLDKAPPPGLPVET-IKDLMRQFLSGLDFLHANCIVHRDLKPENILVTSNGTVK
          IKVTLVFEH..QD..TY.D.A.P.GL..ET..KDLM..F..G.D.L..NCIVHR..KPENILV.S.GTVK
Retrocopy IKVTLVFEHTNQDKQTYMDRAYPAGLQLET<VKDLMHLFQRGPDLLYKNCIVHREPKPENILVLSSGTVK

Parental  LADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGK
          LADF.LARI.S.QMALTP.VVTL...AP..LL.STYATPVD.WSVGCI.AEM....PL..G.SE.DQL.K
Retrocopy LADFDLARICS*QMALTPAVVTLQHHAPGILL*STYATPVDLWSVGCISAEMSGQNPLSYGHSEDDQLDK

Parental  IFDLIGLPPEDDWPREVSLPRGAFAPRGPRPVQSVVPEMEESGAQLL-LEMLTFNPHKRISAFR-ALQHS
          I.D.I.LPPED.WP...SLPR.AF.P....PVQS.V.EMEE..A....LEMLTF..HK.......AL...
Retrocopy ICDQIALPPEDQWPGNISLPR-AFFPKETGPVQSMVTEMEEPRAPSI<LEMLTFEAHKQTCTTE<ALHPC

Parental  YLHK-EESDAE
          .LH..E..DAE
Retrocopy DLHR<EDRDAE

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	26.35 RPM
SRP007412_cerebellum	0.04 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	26.06 RPM
SRP007412_kidney	0.02 RPM	35.73 RPM
SRP007412_liver	0.00 RPM	21.57 RPM
SRP007412_testis	3.61 RPM	15.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1219 was not detected

EST

No EST(s) were mapped for retro_mmus_1219 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_37855	1063 libraries	6 libraries	0 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_1219 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1219 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,