RetrogeneDB ID: retro_ggor_2445

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:80517100..80518315(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSGGOG00000009096
• Aliases: None
• Description: Citrate synthase [Source:UniProtKB/TrEMBL;Acc:G3R145]

Sequence

>retro_ggor_2445
ATGGCTTTACTCACTACTGTCACCCAGTTCTTGGGAACAAAGGACGTATCTTGTCTTGTTCTTGTTGCCTGGCATGCCAG
TACCTCCTCCAGGAATTTGGAAGACATATCGGCTTACCTCATACCCAAGGAGCAGGCCAGAATTAAGATCTCCAGACAGC
AACGTGGCAAGAGGGTGGTGGGCCAAAACACTGTGGGCATGATGTGTGGTGGCCTGAGAGGCAAGAAGGGATTGGTATAT
GAAACATCAGTTCTTGATCCTAATGAAAGCATCCATTTCTGAGGCTTTAGTGTCCCTGAGTGCCAAAAGCTGCCACCCAA
GCCTAAGGGTAAGAAAGAACCCCTGCTGGAGGGTTTATTTCAGCTGCTGGTGGCTGAACAGATCCCAACAGAGGAAACAG
GCATCTTGGCTTTCAAAAAAGTGGGCAAAGAGGACAGCTCTACCCTCCCATATGGTCATCATGCTGGACAACTTTCCCAC
CAATATACATCCCATGTCTCAGCTCAGTGCAGCCTTTACAGCCCTCAACAGTGAAAGTAATACTGCCTGAGCATATGCAG
AGGGTATCAAGTACCGGGAGCTGATTTATGAAGACTGTGTGGATCTGATCACAAAGCTACCTCTGTTGCAGCAAAGATCT
ACCAAAATCTCTACTAAAAGGGCAAAAATGTTGGGGACATTGACTCCAAGCTGCACTGGCCCCACAATTTCACCAACATG
TTAGGTTATACTGATGCTCAGTTCACTGAGCTCATGCATCCGTACCAAACCATCCACAGTGACCATGAGGGCAGCAATGT
AAGTGCCTATATCAGCAACTTGTTGGGCAGTGCCCCTTCAAGCCCTTATCTGTCCTTTGCAACAGCCATGAATGGATTGA
CAGGCCCTCTACGTGTACTAGCAAATCAGGAAGTGCTTGTCTGGCTAACTTAACTACAGAAGGAAGTTGGCAAAGATGTG
GCAGATGAGAAGTTATGAGACTACACCTGGAACACACTCAACCCAGATGAAGTTATTCCAGACTATGGCCATGTAGTGCT
AAAGAAGATTGATCCACGAGGTACCTGCTGTGAGAGTTTGCTCTGAAACACCACATAATGACCCCATGTTAACTTGGTTG
CTCAACTACACAAGATTGTGCTCAATATCGTCTTAGAGAATGGCAAGGCCAAGAATCCTTGGCCCAATGTAGACACACCC
TGGGGTACTGCTCTA

Alignment

ORF - retro_ggor_2445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 87.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYG
          MALLT.....LGTK..SCLVL.A.HAS.SS.NL.DI.A.LIPKEQARIK..RQQ.GK.VVGQ.TV.MM.G
Retrocopy MALLTTVTQFLGTKDVSCLVLVAWHASTSSRNLEDISAYLIPKEQARIKISRQQRGKRVVGQNTVGMMCG

Parental  GMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKSGEEPLPEGLFWLLVTGHIPTEE-QVSWLSK
          G.RG.KGLVYETSVLDP.E.I.F.GFS.PECQKL.PK.K...EPL.EGLF.LLV...IPTEE.Q.SWLSK
Retrocopy GLRGKKGLVYETSVLDPNESIHF*GFSVPECQKLPPKPKGKKEPLLEGLFQLLVAEQIPTEE>QASWLSK

Parental  EWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYAQGISRTKYWELIYEDSMDLIAKL
          .WAKR.ALPSH.V.MLDNFPTN.HPMSQLSAA.TALNSESN.A.AYA.GI...KY.ELIYED..DLI.KL
Retrocopy KWAKRTALPSHMVIMLDNFPTNIHPMSQLSAAFTALNSESNTA*AYAEGI---KYRELIYEDCVDLITKL

Parental  P-CVAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELMRLYLTIHSDHEGGNVSAHTSHLV
          P..VAAKIY.NLY..G...G.IDS.L.W.HNFTNMLGYTD.QFTELM..Y.TIHSDHEG.NVSA..S.L.
Retrocopy P<SVAAKIYQNLY*KGKNVGDIDSKLHWPHNFTNMLGYTDAQFTELMHPYQTIHSDHEGSNVSAYISNLL

Parental  GSALSDPYLSFAAAMNGLAGPLHGLANQ-VLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHA
          GSA.S.PYLSFA.AMNGL.GPL..LANQ.VLVWLT.LQKEVGKDV.DEKL.DY.WNTLN...V.P.YGH.
Retrocopy GSAPSSPYLSFATAMNGLTGPLRVLANQEVLVWLT*LQKEVGKDVADEKL*DYTWNTLNPDEVIPDYGHV

Parental  VLRKTDPRYTCQR-EFALKH-LPNDPMF-KLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLL
          VL.K.DPR.TC...EFALKH...NDPM...LVAQL.KIV.N..LE.GKAKNPWPNVD...G..L
Retrocopy VLKKIDPRGTCCE<EFALKH<PHNDPML<NLVAQLHKIVLNIVLENGKAKNPWPNVDTPWGTAL

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_prefrontal_cortex	0.00 RPM	116.19 RPM
SRP007412_cerebellum	0.00 RPM	97.75 RPM
SRP007412_heart	0.00 RPM	146.34 RPM
SRP007412_kidney	0.00 RPM	129.00 RPM
SRP007412_liver	0.00 RPM	37.61 RPM
SRP007412_testis	0.00 RPM	65.79 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2445 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2445 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3621
Macaca mulatta	retro_mmul_1840

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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,