RetrogeneDB ID: retro_ocun_112

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:50233818..50235324(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000003502
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSOCUG00000015808
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_ocun_112
ATGGGACAGCTGAGCAGCCACATCTTGCAATGGAGAGAAACGCAAACAGTGGATCCGGAGCCGCCAGAAGAACAGGCAGG
CCCCAGCTATATTTGTGGCAGTCGCAAGCGTAAGCGGGGCAGTGGGCCCTCCTTGGGTCCAATGTCTGAAACCCACAGAT
CTCTAAACCAGGGAACCAATCTACACGAAGTCTCCAACACACGCTATGGGAAGAAAGCTAAGATCATATCCAACTGTGCT
TACCGACGTTTATTTTTGAATGGGGAAACCAGTGACATTAAAATCCGTGCTCTGGGGAAGGTATGGTGTTTACACAAAAT
GTTCCTACAGCAATCAGGTTACTTTGCTAATATAATCAGAGATTGTTGGGAAGAATCACAAAATGATATTATTGAGCTGG
ACATTTGTGACCAGAACATAGATGTACAATCTTTGCATTTTGTACTTGGTTCATTATACAGGGACGAATATATTTCAATT
GAGCCCCTTCAAATTCCAGGAGTTCTGGCTGTTGCATACTTGCTTCAATTAGAGGATTTAATTCAGCAATGTGATGAGAC
CATGAAGGAAACAATCAGTGCGAAAACTGTGTGTCGTTATTATGCAGCAGCAGAAACATATGGGTTAGATTCTGTAAAGC
AAACTTGTTTTGAATGGCTTCTCCACAATTTGATGACACAGCCAAGTGTCGAGCTTTACAAAGAAATTGATATAGAGCTC
ATGAATCTTCTCATCTCGTCTCCCAATTTACTAGTAATGCAAAAAGAAATGGATGTATACACGACTCTTAAAGAGTGGGT
GTTCCTTCGCTTCAACCCAGCGTGGAAAGGCTCAATGAAACACCTTTTAGTCACTGCTAACAACTGGCTTTCCAAGTATA
GTGAACAAGTCGATAACATCACTTTTCTTGAAACAAACGAAGGAATAATATTTCAACCAGTATTTAAAACATTGAGGTTT
CAGCATATCATCTGTGACCTGGCAGCCACAAAAGTTATTGAACGAGATAATCTAATACCTTCAGAATGGTTATCAACTGT
TTACAAAAAAAAATGGCTTTCCTTCCTACGAGCACAGCAGTGCAGGGAAATTGGGCCTCGACACATCAATAAAGCAGAAC
TTGAAGGGTATAGCATGAGATGTGGTAAAAGGATTGTCAAGGATGGAAGATACTCCTGGAAGTGGTCAGGTTACAACTTC
GGCTTTCCTTTACACGTCATCTTTACCAGCCATTATATAATTTTCAAACAAAATACTTTCAGGCAGCTATGTGAGGGTTC
TGCCTGTACACAATGTATACGAAATATTGCCTTCAGATTAACCTTGGCATATTTCGATTCTAGTGGGAATCTAAGCTTCA
GCAAAACAACTGGTTATAAAATCCTGACTTTTGAAAAGGATGAAGAACAAGTGGTAATGAATTTGGATAGTGTTGTTCTG
AACTTCCCTTTATATATTTTCTGTAACTTCCTGTTTATGTCATCAGAAAATACAGGAAACTTATAA

Alignment

ORF - retro_ocun_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 89.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRKRKQSSGAFYYHPDSETDEDEEEGDEQQRLLNTPRSRKKLKSTSKYIYQTLFLNGENSDIKICALGEE
          SRKRK..SG.....P.SET......G.......NT.R..KK.K..S...Y..LFLNGE.SDIKI.ALG..
Retrocopy SRKRKRGSGPSL-GPMSETHRSLNQGTNLHEVSNT-RYGKKAKIISNCAYRRLFLNGETSDIKIRALGKV

Parental  WSLHKIYLCQSGYFSSMFSGSWKESNMNIIELEIPDQNIDIEALQVAFGSLYRDDVL-IKPSRVIAILAA
          W.LHK..L.QSGYF.......W.ES...IIEL.I.DQNID...L....GSLYRD....I.P......LA.
Retrocopy WCLHKMFLQQSGYFANIIRDCWEESQNDIIELDICDQNIDVQSLHFVLGSLYRDEYISIEPLQIPGVLAV

Parental  ACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVM
          A..LQL..LIQQC.ETMKETI..KTVC.YY..A.TYGLDSVK..C.EWLL.NLMT...VEL.KE..I..M
Retrocopy AYLLQLEDLIQQCDETMKETISAKTVCRYYAAAETYGLDSVKQTCFEWLLHNLMTQPSVELYKEIDIELM

Parental  KQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRKKVDFEGMTFLETEQGKP
          ..LI.S.NL.VMQ.EMDVYT.LK.W.FL...P.W.GS.K.LL.....W.SK.........TFLET..G..
Retrocopy NLLISSPNLLVMQKEMDVYTTLKEWVFLRFNPAWKGSMKHLLVTANNWLSKYSE-QVDNITFLETNEGII

Parental  FVSVFKHLRLQYIISDLASAKIIEQDSLVPSEWLSCVYKQQWLAMLRAEQDSEVGPQEINKEELEGNSMR
          F..VFK.LR.Q.II.DLA..K.IE.D.L.PSEWLS.VYK..WL..LRA.Q..E.GP..INK.ELEG.SMR
Retrocopy FQPVFKTLRFQHIICDLAATKVIERDNLIPSEWLSTVYKKKWLSFLRAQQCREIGPRHINKAELEGYSMR

Parental  CGRKLTKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGK
          CG....KDG.Y.W.W.G.NFGF.L.V..T..YIIFK.NT..Q.C.GS...Q..R.IAFRL.LA.FDSSG.
Retrocopy CGKRIVKDGRYSWKWSGYNFGFPLHVIFTSHYIIFKQNTFRQLCEGSACTQCIRNIAFRLTLAYFDSSGN

Parental  LICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYISSE
          L..S.TTGY.ILT.EKD.EQVVMNLDS..L.FPLYI.CNFL..SSE
Retrocopy LSFSKTTGYKILTFEKDEEQVVMNLDSVVLNFPLYIFCNFLFMSSE

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
SRP017611_brain	0.00 RPM	11.48 RPM
SRP017611_kidney	0.00 RPM	31.22 RPM
SRP017611_liver	0.00 RPM	18.73 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_112 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_112 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,