RetrogeneDB ID: retro_mmus_16

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:95025444..95026194(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071722
• Aliases: Spin4, 9630042H07Rik
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Spin1
• Ensembl ID: ENSMUSG00000021395
• Aliases: Spin1, Spin
• Description: spindlin 1 [Source:MGI Symbol;Acc:MGI:109242]

Sequence

>retro_mmus_16
ATGTCTCCTCCGACTGTGCCTCCTACTGGGGTGGATGGTGTGTCCGCGTACCTGATGAAGAAAAGGCACACTCACAAGAA
GCAGCGCCGTAAGCCCACTTTCCTCACTCATAGGAACATCGTGGGCTGCCGCATTCAACACGGCTGGAAAGAAGGCAATG
AGCCCGTGGAGCAATGGAAAGGTACTGTGCTCGAGCAGGTCTCCGTGAAGCCCACTCTGTATATCATCAAATATGATGGC
AAAGACAGTGTGTACGGACTGGAACTGCACAGAGATAAGAGAGTTTTAGCGCTGGAGATTCTTCCTGAGAGAGTTCCTTC
TCCTCGCATTGACTCTCGCCTGGCCGATTCCCTGGTTGGGAAGGCAGTGGGACATGTGTTCGAAGGTGAGCATGGCAAGA
AAGATGAGTGGAAGGGTATGGTGTTGGCGCGAGCCCCCATCATGGATACTTGGTTTTACATCACCTACGAGAAAGATCCG
GTCCTCTATATGTACACCCTGCTGGACGACTACAAAGATGGTGACCTGCGTATCATTCCAGATTCCAACTACTACTTCCC
TGCAGCTGAACAGGAGCCTGGGGAGGTGCTCGACAGCCTTGTGGGCAAGCAGGTGGAACACGCCAAAGACGACGGGTCCA
AGAGAACTGGGATCTTTATTCATCAGGTGGTAGCCAAGCCATCTGTCTACTTCATTAAGTTTGATGATGATATTCACATT
TATGTCTATGGCTTGGTGAAAACCCCGTAA

Alignment

ORF - retro_mmus_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 87.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKHRTSVGPSKPVSQPRRNIVGCRIQHGWREGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELN
          K.H.......KP.....RNIVGCRIQHGW.EGN.PV.QWKGTVL.QV.V.P.LY.IKYDG.D.VYGLEL.
Retrocopy KRHTHKKQRRKPTFLTHRNIVGCRIQHGWKEGNEPVEQWKGTVLEQVSVKPTLYIIKYDGKDSVYGLELH

Parental  KDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKD
          .D.RV.ALE.LP.RV...RI.D..LAD...GKAV.H.FE.E.G.KDEW.GMVLARAP.M.TWFYITYEKD
Retrocopy RDKRVLALEILPERVPSPRI-DSRLADSLVGKAVGHVFEGEHGKKDEWKGMVLARAPIMDTWFYITYEKD

Parental  PVLYMYQLLDDYKEGDLRIMPDSN-DSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSV
          PVLYMY.LLDDYK.GDLRI.PDSN...P.AE.EPGEV.DSLVGKQVE.AK.DGSKRTG..IHQV.AKPSV
Retrocopy PVLYMYTLLDDYKDGDLRIIPDSNYYFPAAEQEPGEVLDSLVGKQVEHAKDDGSKRTGIFIHQVVAKPSV

Parental  YFIKFDDDFHIYVYDLVKT
          YFIKFDDD.HIYVY.LVKT
Retrocopy YFIKFDDDIHIYVYGLVKT

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	0.14 RPM	167.51 RPM
SRP007412_cerebellum	0.43 RPM	95.61 RPM
SRP007412_heart	0.53 RPM	31.35 RPM
SRP007412_kidney	0.48 RPM	70.16 RPM
SRP007412_liver	0.14 RPM	54.51 RPM
SRP007412_testis	0.09 RPM	23.42 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_16 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	X:95026408..95026966
ENCFF001YIJ	POLR2A	X:95026168..95027052

EST

No EST(s) were mapped for retro_mmus_16 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_158571	239 libraries	294 libraries	410 libraries	117 libraries	12 libraries

The graphical summary, for retro_mmus_16 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_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_16 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_281

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003301	4 retrocopies	retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus	ENSBTAG00000003044	4 retrocopies	retro_btau_1678, retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris	ENSCAFG00000002208	3 retrocopies	retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni	ENSCHOG00000006983	2 retrocopies	retro_chof_1343, retro_chof_1852,
Callithrix jacchus	ENSCJAG00000017452	1 retrocopy	retro_cjac_227,
Cavia porcellus	ENSCPOG00000000743	1 retrocopy	retro_cpor_123,
Echinops telfairi	ENSETEG00000013719	1 retrocopy	retro_etel_28,
Felis catus	ENSFCAG00000007197	2 retrocopies	retro_fcat_32, retro_fcat_70,
Homo sapiens	ENSG00000106723	1 retrocopy	retro_hsap_64,
Loxodonta africana	ENSLAFG00000027497	2 retrocopies	retro_lafr_18, retro_lafr_58,
Microcebus murinus	ENSMICG00000014510	1 retrocopy	retro_mmur_8,
Myotis lucifugus	ENSMLUG00000008516	2 retrocopies	retro_mluc_132, retro_mluc_1626,
Mustela putorius furo	ENSMPUG00000008585	1 retrocopy	retro_mputfur_139,
Mus musculus	ENSMUSG00000021395	3 retrocopies	retro_mmus_112, retro_mmus_16 , retro_mmus_3351,
Oryctolagus cuniculus	ENSOCUG00000011880	1 retrocopy	retro_ocun_63,
Otolemur garnettii	ENSOGAG00000002166	2 retrocopies	retro_ogar_2327, retro_ogar_9,
Procavia capensis	ENSPCAG00000015800	1 retrocopy	retro_pcap_14,
Pongo abelii	ENSPPYG00000019355	1 retrocopy	retro_pabe_33,
Pan troglodytes	ENSPTRG00000021088	2 retrocopies	retro_ptro_116, retro_ptro_95,
Pteropus vampyrus	ENSPVAG00000013391	3 retrocopies	retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus	ENSRNOG00000011119	4 retrocopies	retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus	ENSSTOG00000029107	1 retrocopy	retro_itri_136,
Tursiops truncatus	ENSTTRG00000005602	6 retrocopies	retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,