RetrogeneDB ID: retro_mmul_1840

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:76627778..76629118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.467
• Ensembl ID: ENSMMUG00000002483
• Aliases: None
• Description: Citrate synthase [Source:UniProtKB/TrEMBL;Acc:F7HGU4]

Sequence

>retro_mmul_1840
ATGGCTTTACTCACTGCTGCCACCCAGTTCTTGGGAACAAAGGATGTATCTTGTCTTGTTCTTGCTGCCTGGCATGCCAG
TACCTCCTCTAGGAATTTGGAAGACATATTGACTTACCTGATACCCAAGGAGCAGGCCAGAATTAAGATCTTCAGACAGC
AAAGTGGCAAGAGGGTGGTGGGCCAAACCACTGTGGGCAGGATGTGTGGTGGCCTGAGAGGCACGAGGGGATTGGTATAT
GAAACATCAGTTCTTGATCCTAATGAAAGCATCCATTTCTGAGGCTTTAGTGTCCCTGAGTGCCAAAAACTGCCACCTAA
GGCTAAGGGTAAGAAAGAACCTCTGCTGGAGGGCTTATCTCAGCTGCTGGTAGCTGAACATATCCCAACAGAGGAAACAG
GTATCCTGGCTTTCAAAAAAGTGATCAAAGAGGGCAGCTCTACCCTCCCATGTGGTCACCATGCTGGACAACTTTCCCAC
CAATATACATCCCATGTCTCAGCTCAGTGCAGCCTATACAGCCCTCAACAGTGAAAGTAATACTACCTGAGCATATGCAG
AGGATATCAAGTTCTGGGAGCTGATTTATGAAGACTGTGTGGATCTGATCACAAAGCTACCTGTGTTGCAACAAAGATCT
ACCAAAATCTCTACTAAGAGGGCAAAAATGTTGGGGCCATTGACTCCAAGTTGAACTGGTCCCACAATTTCACCAACATG
TTAGGCTATACTGATGCTCAGTTCACTGAGCTCACGCACCTGTACCACACCATCCACAGTGACCATGAGGGCAGCGATGT
AAGTGCCCATATCAGCAACTTGTTGGGCAGTGCCCCTTCAAGCCCTTATCTGTCCTTTGCAACAGCCATGTATGGATTGA
CAGGCCCTCTACATGTACTAGCAAATCAAGAACTGTTTGTCTGGCTAACTCAACTACAGAAGGAAACTGGCAAAGATGTG
GCATGTGAGAAGTTATGAGACTACACCTGGAACACACTCAACCTAAGATGAAGTTATTCCAGACTGTGACCATGCAGTAT
TAAAGAAGACTGATCCATGAGATACCTGCAGTGACAGTTTGCTCTGAAACACCACATAATGACCCCATGTTAACTTGGTT
GCTCAGCTACACAAGATTGTGCTCAATAGCCTCTTAGAGAATGGCAAAGCCAAGAATACTTGGCCCAATGTAGACACACC
CTGGGGTACTGCTCCAGGACTATGGCATGATGGAAATGAATTACTACACTGTTTGGTTCAGAGTGTCTCGGGCACTGAGT
GTACTGGCACAGCTCATCTGAAGTCATGCACTCGGATTCTCTCTAGAAAGGCCCAAGTCT

Alignment

ORF - retro_mmul_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 96.78 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYG
          MALLTAA...LGTK..SCLVLAA.HAS.SS.NL.DIL..LIPKEQARIK.FRQQ.GK.VVGQ.TV..M.G
Retrocopy MALLTAATQFLGTKDVSCLVLAAWHASTSSRNLEDILTYLIPKEQARIKIFRQQSGKRVVGQTTVGRMCG

Parental  GMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEE-QVSWLSK
          G.RG..GLVYETSVLDP.E.I.F.GFS.PECQKL.PKAKG..EPL.EGL..LLV...IPTEE.QVSWLSK
Retrocopy GLRGTRGLVYETSVLDPNESIHF*GFSVPECQKLPPKAKGKKEPLLEGLSQLLVAEHIPTEE>QVSWLSK

Parental  EWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYAEGISRTKYWELIYEDSMDLIAKL
          ...KRAALPSHVVTMLDNFPTN.HPMSQLSAA.TALNSESN...AYAE.I...K.WELIYED..DLI.KL
Retrocopy K*SKRAALPSHVVTMLDNFPTNIHPMSQLSAAYTALNSESNTT*AYAEDI---KFWELIYEDCVDLITKL

Parental  P-CIAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDSQFTELMRLYLTIHSDHEGGNVSAHTSHLV
          P.C.A.KIY.NLY.EG...GAIDS.L.WSHNFTNMLGYTD.QFTEL..LY.TIHSDHEG..VSAH.S.L.
Retrocopy P<CVATKIYQNLY*EGKNVGAIDSKLNWSHNFTNMLGYTDAQFTELTHLYHTIHSDHEGSDVSAHISNLL

Parental  GSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNS-GRVVPGYGH
          GSA.S.PYLSFA.AM.GL.GPLH.LANQE..VWLTQLQKE.GKDV..EKL.DY.WNTLN....V.P...H
Retrocopy GSAPSSPYLSFATAMYGLTGPLHVLANQELFVWLTQLQKETGKDVACEKL*DYTWNTLNL>DEVIPDCDH

Parental  AVLRKTDPRYTC-QREFALKH-LPNDPMF-KLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSG-VLLQYYG
          AVL.KTDP..TC.Q..FALKH...NDPM...LVAQL.KIV.N.LLE.GKAKN.WPNVD...G..L..Y.G
Retrocopy AVLKKTDP*DTC<Q*QFALKH<PHNDPML<NLVAQLHKIVLNSLLENGKAKNTWPNVDTPWG>LLQDY-G

Parental  MTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKS
          M.EMNYYTV.F.VSRAL.VLAQLI.S.ALGF.LERPKS
Retrocopy MMEMNYYTVWFRVSRALSVLAQLI*SHALGFSLERPKS

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	176.93 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	155.33 RPM
SRP007412_cerebellum	0.00 RPM	180.42 RPM
SRP007412_heart	0.06 RPM	361.91 RPM
SRP007412_kidney	0.00 RPM	234.62 RPM
SRP007412_liver	0.00 RPM	53.68 RPM
SRP007412_testis	0.00 RPM	57.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1840 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1840 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3621
Gorilla gorilla	retro_ggor_2445

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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,