RetrogeneDB ID: retro_meug_1078

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold27962:11166..11973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSMEUG00000005657
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_meug_1078
CTGATTTAGGAGGACTACATGGATCTCATTTCCAAGCTACCTTGTGTTGCAGAAAAAAATCTACCGGAATCTCTATCATG
AAGGCAGCAACATTGGGGTTATAGACAACAAAACTGACTGGTCTCATGACTTTACCAGAATGTCAGGCTACAGTGATGCC
CAGTTTACTGAGCTCATGTGCTTATTCCTGACATTCCACAGGGATCACAAGGATTGCAATGTAAATGTCCACACTAGCCA
TCCGGTAGGCAGTGCTCTTTCAGATCCCTATCTATCCTTTGCAGCTGTTAAGAATGGACTGGCTGGGCCCCTCCATGAAT
TAGTCAATTAGGAAGTACTCATCTGGCTGAAACAGTTGCAGAAAAAAGTGGGCAAAGAAGTAGCTAATGAAAAACCATGT
GACTACATGTGGAACACACTGAACTCAGGCAGAGTGGTCTCTGGCTACGGCCATGCTGTTCGAAGAAAAACTGATCCACA
ATATACCTGTCAGCAAGAATTTGCTCTGAAACATATACCTAATGATCCTATGTTTAAACTAGTGCCTCAACTTTATAAAA
TTGTACCTGATCTCCTTTTCAAGCAGGTCAAAGCCAAGAACCCCTGACCCAATGTAGATGCCCACAGTGTGGTGCTTCTG
CAGTACTATGGCATGACAGAGATGAATTACTAGACAGCTCTTTTTGGAGTTTCATTGGTGCTGAGATGCTGGCACAGTTC
TTTTGTAGCAGAGCTCTGGGCTTCCCCCTGGAAAGGCCAAAATCTATGAGCACAGATAGCTTGATGCAATTTGTAAGGTC
AAAGTCG

Alignment

ORF - retro_meug_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.86 %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIYEDCMDLIAKLPCVAAK-IYRNLYREGSSIGAIDTKLDWSHNFTSMLGYSDAQFTELMRLYLTIHSDH
          LI.ED.MDLI.KLPCVA.K.IYRNLY.EGS.IG.ID.K.DWSH.FT.M.GYSDAQFTELM.L.LT.H.DH
Retrocopy LI*EDYMDLISKLPCVAEK>IYRNLYHEGSNIGVIDNKTDWSHDFTRMSGYSDAQFTELMCLFLTFHRDH

Parental  EGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKEVDDEKLRDYIWNT
          ...NV..HTSH.VGSALSDPYLSFAA..NGLAGPLH.L.N.EVL.WL.QLQK.VGKEV..EK..DY.WNT
Retrocopy KDCNVNVHTSHPVGSALSDPYLSFAAVKNGLAGPLHELVN*EVLIWLKQLQKKVGKEVANEKPCDYMWNT

Parental  LNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPNDPMFKLVAQLYKIVPDVLLEQGKAKNPWPNVDAHS
          LNSGRVV.GYGHAV.RKTDP.YTCQ.EFALKH.PNDPMFKLV.QLYKIVPD.L..Q.KAKNP.PNVDAHS
Retrocopy LNSGRVVSGYGHAVRRKTDPQYTCQQEFALKHIPNDPMFKLVPQLYKIVPDLLFKQVKAKNP*PNVDAHS

Parental  GVLLQYYGMTEMNYYTVLFGVSRAL-GVLAQLIWSRALGFPLERPKSMSTDGLMQFVSSKS
          .VLLQYYGMTEMNY.T.LFGVS..L...LAQ...SRALGFPLERPKSMSTD.LMQFV.SKS
Retrocopy VVLLQYYGMTEMNY*TALFGVSLVL<EMLAQFFCSRALGFPLERPKSMSTDSLMQFVRSKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1078 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1078 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078 , retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,