RetrogeneDB ID: retro_mmus_3665

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:94997393..94998704(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000087522
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gmcl1
• Ensembl ID: ENSMUSG00000001157
• Aliases: Gmcl1, 2810049L19Rik, Gcl, mglc-1
• Description: germ cell-less homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:1345156]

Sequence

>retro_mmus_3665
AAAGTACCCCGTAGGACACTGTATGAATCACTGTTCCTGAGGGGTGAAAATAGCGATATAAAGATCTGTGCGTTTCAGGA
GGAGTGGCATTTGCACAAGTCCTATCTGTGCCGCTCTGGGTACTTTTCTAGCATGTTCTGTGGGGCCTGGCGAGAGTCAA
ATATGGATACGATAGAGATGCAGATGCCCGATGAAAATATTGATCGCGAGGCTTTCAATGATGTTCTAGGCTTCTTGTAC
AGTCGAAGAATTGTAATTCCTCCCCCTCGAGTCATTGCCGTCTTGGCCACAGCGAATATGCTGCAATTGGATGAGTTAAT
TCAGCAGTGTGAGGATATGATGAGAGCCTCAGTCAGTACCGAGACTGTGTGCAACTACTACTACTCTGCTGAGAATTACG
GGCTCCAGAGCATCAAATATGTTTGCTGCCAGTGGCTCTTGGACAACCTGATGACCCGAAAAAATGATGAACTATTGTTA
GGAATCAGTGTGGATCTCATGAAAGAGCTCATTGCCTCTTCAGATCTTTTGGTGGTTGGAGTGGAGATGGATGTGTATAT
TACACTGAAAACGTGGATGTACCTGCAGCTGGAAGCACGCACATGCTCAGGATCTGAAAGAGTATTACTGCCTGAAGAGT
TGAGCTTTGCAAAGTTCAGAAGGGAGTCAGATAACAGACCTTTTCTGGACAGTGATCAGGGGAGAGCCTTTGTGTCAGTG
TTCCAGCGACTAAGGCTTCCCTACATCATCAGTGACCTGCCTTCAGCACGCATTATTGAACAGGATAGACTGATCCCTGC
AGCATGGTTGACTCCAGTATACAAAGAGCAATGGCTAGCACTTCTTCAGGCAGAGCAGTCCAGGGAACTTGGGCGAATGG
ATATCAATGTGTCTGACATCCATGGAAACAGCATGAGGTGTGGAGGCCAACTTTTCACAGATGAGCAATGCAGCTGGACC
TGGTCTGGCTTCAACTTTGGCTGGGACTTGGTAGTGTGCTATAACAACAGGCGCATTATATTATGTCGCAGTGCAATGAA
TAAATCCTGTGGCCTTGGTGTCAGCTTACTCTGGCAGAGAAAAATTGCCTTCCGTCTACGAGTGATCTCATTGGACAGTA
CTGGAAAATCTGTTCTCAGAAGAGAGACTGACTATAATATTCTTTCTCTGAGAAAGAATCAACAACTAGAAGTGGTGAAC
CTCGGAAACCAAGATATAATTTTCCCCATATATGTGGCATGCAACTTCCTCTACCTTCCTGGAGAGAGTAGCGCTGGACC
AAGTGGGGAATCAAGCAGAAGTCCAATAAAC

Alignment

ORF - retro_mmus_3665 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.95 %
• Parental protein coverage: 82.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIE
          K......Y..LFL.GENSDIKICA..EEW.LHK.YLC.SGYFSSMF.G.W.ES.M..IE...PD.NID.E
Retrocopy KVPRRTLYESLFLRGENSDIKICAFQEEWHLHKSYLCRSGYFSSMFCGAWRESNMDTIEMQMPDENIDRE

Parental  ALQVAFGSLYRDDVLIKPSRVVAILAAACMLQLDGLIQQCGETMKETISVRTVCGYYTSAGTYGLDSVKK
          A.....G.LY.....I.P.RV.A.LA.A.MLQLD.LIQQC...M....S..TVC.YY.SA..YGL.S.K.
Retrocopy AFNDVLGFLYSRRIVIPPPRVIAVLATANMLQLDELIQQCEDMMRASVSTETVCNYYYSAENYGLQSIKY

Parental  KCLEWLLNNLMTHQSVELFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLT
          .C..WLL.NLMT....EL....S...MK.LI.SS.L.V..VEMDVY..LK.WM.LQL...........L.
Retrocopy VCCQWLLDNLMTRKNDELLLGISVDLMKELIASSDLLVVGVEMDVYITLKTWMYLQLEARTCSGSERVLL

Parental  ETDVWFSKWKKDFEGTTFLETEQGKPFAPVFRHLRLQYIISDLASARIIEQDSLVPSEWLAAVYKQQWLA
          .....F.K.........FL...QG..F..VF..LRL.YIISDL.SARIIEQD.L.P..WL..VYK.QWLA
Retrocopy PEELSFAKFRRESDNRPFLDSDQGRAFVSVFQRLRLPYIISDLPSARIIEQDRLIPAAWLTPVYKEQWLA

Parental  MLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPC
          .L.AEQ..E.G...IN.....GNSMRCG..L..D....W.W.GFNFG.DL.V.Y.NR.II..R...N..C
Retrocopy LLQAEQSRELGRMDINVSDIHGNSMRCGGQLFTDEQCSWTWSGFNFGWDLVVCYNNRRIILCRSAMNKSC

Parental  SGSVSLQPRRSIAFRLRLASFDSSGKLICSRATGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYIS
          ...VSL...R.IAFRLR..S.DS.GK....R.T.Y.IL.L.K.Q...V.NL.....IFP.Y..CNFLY..
Retrocopy GLGVSLLWQRKIAFRLRVISLDSTGKSVLRRETDYNILSLRKNQQLEVVNLGNQDIIFPIYVACNFLYLP

Parental  PEKRT----ESNRHPEN
          .E.......ES.R.P.N
Retrocopy GESSAGPSGESSRSPIN

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	0.05 RPM	28.04 RPM
SRP007412_cerebellum	0.04 RPM	23.40 RPM
SRP007412_heart	0.28 RPM	5.35 RPM
SRP007412_kidney	0.02 RPM	20.56 RPM
SRP007412_liver	0.00 RPM	12.32 RPM
SRP007412_testis	0.64 RPM	112.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3665 was not detected

EST

No EST(s) were mapped for retro_mmus_3665 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_158570	1057 libraries	11 libraries	2 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_3665 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_3665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665 ,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,