RetrogeneDB ID: retro_mmus_1265

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:40294700..40295530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cap1
• Ensembl ID: ENSMUSG00000028656
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein 1 (yeast) [Source:MGI Symbol;Acc:MGI:88262]

Sequence

>retro_mmus_1265
ATGGCAGACATGCATAATCTTGTAGAAAGATTGGAGAGGGCAGTGGGCTCCCTGGAGGCAGTGTCATGTACCTCTGACAT
GCACTGTGGGTAAGGAGACAGTCTGTCAAGAGGAGCAGTTCCATATGTGCAAGCATTTGACTTGCTGCTTGCCAAGTCCA
TGGCAGAATACATGAAGGTGAGTAAGGAGGTTGGGGGAGACATGCAGAAACGTGTGGAGAAGGTCCACATAAGCCTGAAT
TTGAAGCGAGCTTTCCTGATTACGGCTTCTCAGTGGCAGCAGCCAGCCAGTAGTAAACTTTCTGATTTGTTGATAACTTT
CTCAGAGCTGATCCAAGAAGTTGTACCTTCTGGGAGAAGAGCCGAGACAGCAAAATTTTCAATCATGTATCAGCTGTCAG
TGAAAGCATCCAGACCCTGGGCTGGGTGGCTCTGGCTGAGAAACCTGGGCCTGTTATGAAAGAGATGAATGGTGTGGCCA
TGTTTTAAATGAACCAAGTCCTCATGGGATACAGAGATCTGGATAAGAAGCCTGTGGACTAGGACAGAGCTTACTTGAAT
ATATTGACAGAACTGCAGGCTTACATTAACTAGTTCCATACCAATGGCCTGCCCTAGGGCAAGATGGAGCCAATGGCAAA
AGAACCGAGTGGATGGCCATATGGACCTTCTGTGGGATCAAGCCCACTTCCTCTCCTACTAGGCTTGCCTCTTTCCCCAG
TCCCTACCTGTTCTGGCTCTGAGGACTCCACTTCATGCTCAGCACTGTTTGCACAGATTAATTAAAGAGAGAACATCACA
CACGCCCTGAATCATGTATCTGATGTCATG

Alignment

ORF - retro_mmus_1265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.42 %
• Parental protein coverage: 58.44 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVERLERAVGRLEAVSHTSDMHCGYGDSPSKGAVPYVQAFDSLLANPVAEYLKMSKEIGGDVQK
          MADM.NLVERLERAVG.LEAVS.TSDMHCG.GDS.S.GAVPYVQAFD.LLA...AEY.K.SKE.GGD.QK
Retrocopy MADMHNLVERLERAVGSLEAVSCTSDMHCG*GDSLSRGAVPYVQAFDLLLAKSMAEYMKVSKEVGGDMQK

Parental  HAEMVHTGLKLERALLATASQCQQPAGNKLSDLLAPISEQIQEVI-TFREKNRGSKFFNHLSAVSESIQA
          ..E.VH..L.L.RA.L.TASQ.QQPA..KLSDLL...SE.IQEV..TF.EK.R.SK.FNH.SAVSESIQ.
Retrocopy RVEKVHISLNLKRAFLITASQWQQPASSKLSDLLITFSELIQEVV<TFWEKSRDSKIFNHVSAVSESIQT

Parental  LGWVALAAKPGPFVKEMNDAAMFYTNRVLKEYRDVDKKHVDWVRAYLSIWTELQAYIKEFHTTGLAWSKT
          LGWVALA.KPGP..KEMN..AMF..N.VL..YRD.DKK.VD..RAYL.I.TELQAYI..FHT.GL...K.
Retrocopy LGWVALAEKPGPVMKEMNGVAMF*MNQVLMGYRDLDKKPVD*DRAYLNILTELQAYIN*FHTNGLP*GKM

Parental  GPVAKELSGLPSGPSVGSGPPPPPPGPPPPPISTSSGSDDSASRSALFAQINQGESITHALKHVSDDM
          .P.AKE.SG.P.GPSVGS.P.P...G.P..P..T.SGS.DS.S.SALFAQIN..E.ITHAL.HVSD.M
Retrocopy EPMAKEPSGWPYGPSVGSSPLPLLLGLPLSPVPTCSGSEDSTSCSALFAQIN*RENITHALNHVSDVM

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	212.21 RPM
SRP007412_cerebellum	0.00 RPM	133.74 RPM
SRP007412_heart	0.00 RPM	52.98 RPM
SRP007412_kidney	0.00 RPM	136.98 RPM
SRP007412_liver	0.00 RPM	74.83 RPM
SRP007412_testis	0.00 RPM	120.16 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1265 was not detected

EST

No EST(s) were mapped for retro_mmus_1265 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_34479	238 libraries	365 libraries	441 libraries	26 libraries	2 libraries

The graphical summary, for retro_mmus_1265 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_1265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1265 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1180

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265 ,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,