RetrogeneDB ID: retro_cjac_2031

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:37362821..37364220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSCJAG00000011275
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_cjac_2031
ATGGCTTTACTCACTGTGGCTGTCCAGCTCTTGGGAACCAAGAATACACCTTGTCTTGTTCTTGCTGTTCAGCACGCCAG
TGCTTCCTCCACGAATTCGAAAGACACATTGGCTGACCTGATTCCTAAGGAGCAGGCCAGAATCAAGCCCTTCAGGCAGC
AATATGGCAAGACAGCGTTAGACCCAATCACTGTGGGCACGATGCGTGGTGGTGTCAGAGGCGCACAGGGCGCGGTCTGT
GAAACATCAGTTCTTGATCCTGATGACGGCATCCGTTTCTGAGGCTTTAGCATCCCTGAAGGCCAAAAAGTGCTACCCAA
GGCTAAGGGTGGGGACCCCTGCCCGAGGGCTTATTTTGGCTGCTGGTAACTGGACAGATTCCAACAGAGGAACAGGTATC
TGGGCTCTCAAAACAGTGGGCAAAGTGGGCAGCTCTGCCTTCCCATGTGGTCACCACGCTGGACAGCTTTCCCACCAATC
TACACCCACATCTCAGCTCAGTGCAGCCGGTACAGCCTCAACCATGAAAGTAACTTTGCCTGAGCGTATGCAGAGGTATC
AACCAAACCAAGTACTAGGAGCTGGTTCCTGAAGACTCTATGGATCTACTGGCAAAGCTACCGTGTGTTGCAGCAAAGAT
CTACCGACATCTCTACAGAGAAGGCGGCAGTATTGCGGCCATTGATTCTAAGCTGGACTGGCCCCACAGTTTCACCAACG
TGTTGGACTATACTGATGGGCTATACTAACATGAGTTCACTGAGCTCATGCACCTCTACTCACCATCCACAGTGACCATG
AGGGTGGCCATGTAAATGCCCATACCAGCCACTTGGTGGGCAGTGCCCATTCAGACCCTTACCTTCCTTTGCAGCAGCCG
TGAACAGGCTGCCAGGGCCTCTCCAGGGACTGGCAAATCAGGAAGTGCTTGTCTGGTTAACACAGCTACAGAAGGAAGTT
GGTGAAGATGCATCAGATGAGAACTACCAGACCACATCTGGAACACACTCAACTCGGGATGGGTTTTCCCAGGCTATGGC
CAGGCAGTACTAAGGAAACTAATCCACGATATACCCATCAGTGAGAGTTTGCTCTGAAACACCTGCCTAATGATCCCACG
TGTAAGTTGGTTGCTCAGCTATATGAGATTATGCTCAATGTCCTCTTAGAGCAAGGTAAGGTCAAGAATCCTTGGCCCAA
TGTAGGTGGTCACAGTGGGGTGCTGCTCCACTACTGTGGTATGATGGAGATGACCTACTACACGGTCCTGTGTGGGGTGT
CACAAGCATTGGGTGTATTGGCACAGCTCATCTGGAGCCGAGCCGTAGGCTTCCCTCTAGAAAGACCCAAGTCCGTGATC
ACAGAGGGTCTGATGAAGTTGGTAGACTCTAAGTCAGGG

Alignment

ORF - retro_cjac_2031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MALLTAAARLLGTKNASCLVLASRHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYG
          MALLT.A..LLGTKN..CLVLA..HASASSTN.KD.LADLIPKEQARIK.FRQQ.GKT....ITV..M.G
Retrocopy MALLTVAVQLLGTKNTPCLVLAVQHASASSTNSKDTLADLIPKEQARIKPFRQQYGKTALDPITVGTMRG

Parental  GMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLP-EGLFWLLVTGQIPTEEQVSWLSK
          G.RG..G.V.ETSVLDPD.GIRF.G.SIPE.QK.LPKAKGG..P.P.EGLFWLLVTGQIPTEEQVS.LSK
Retrocopy GVRGAQGAVCETSVLDPDDGIRF*GFSIPEGQKVLPKAKGG-DPCP<EGLFWLLVTGQIPTEEQVSGLSK

Parental  EWAKRAALPSHVVTMLDNFPTNLH-PMSQLSAAVTA-LNSESNFARAYAE-GISRTKYWELIYEDSMDLI
          .WAK.AALPSHVVT.LD.FPTNLH.P.SQLSAA.TA.LN.ESNFA.AYAE.GI..TKY.EL..EDSMDL.
Retrocopy QWAKWAALPSHVVTTLDSFPTNLH<PTSQLSAAGTA<LNHESNFA*AYAE<GINQTKY*ELVPEDSMDLL

Parental  AKLPCVAAKIYRNLYREGSGIGAIDSKLDWSHNFTNMLGYTDA----QFTELMRLY-LTIHSDHEGGNVS
          AKLPCVAAKIYR.LYREG..I.AIDSKLDW.H.FTN.L.YTD......FTELM.LY.LTIHSDHEGG.V.
Retrocopy AKLPCVAAKIYRHLYREGGSIAAIDSKLDWPHSFTNVLDYTDGLY*HEFTELMHLY<LTIHSDHEGGHVN

Parental  AHTSHLVGSALSDPYL-SFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDE-KLRDYIWNTLNSG
          AHTSHLVGSA.SDPYL.SFAAA.N.L.GPL.GLANQEVLVWLTQLQKEVG.D.SDE..L.D.IWNTLNSG
Retrocopy AHTSHLVGSAHSDPYL<SFAAAVNRLPGPLQGLANQEVLVWLTQLQKEVGEDASDE<ELPDHIWNTLNSG

Parental  RVVPGYGHAVLRK-TDPRYTCQREFALKHLPNDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVL
          .V.PGYG.AVLRK.T.PRYT.Q.EFALKHLPNDP..KLVAQLY.I..NVLLEQGK.KNPWPNV..HSGVL
Retrocopy WVFPGYGQAVLRK<TNPRYTHQ*EFALKHLPNDPTCKLVAQLYEIMLNVLLEQGKVKNPWPNVGGHSGVL

Parental  LQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG
          L.Y.GM.EM.YYTVL.GVS.ALGVLAQLIWSRA.GFPLERPKS..TEGLMK.VDSKSG
Retrocopy LHYCGMMEMTYYTVLCGVSQALGVLAQLIWSRAVGFPLERPKSVITEGLMKLVDSKSG

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
SRP051959_colon	0.02 RPM	73.35 RPM
SRP051959_heart	0.00 RPM	106.29 RPM
SRP051959_kidney	0.00 RPM	64.01 RPM
SRP051959_liver	0.02 RPM	25.41 RPM
SRP051959_lung	0.03 RPM	37.37 RPM
SRP051959_lymph_node	0.05 RPM	31.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	144.68 RPM
SRP051959_spleen	0.00 RPM	34.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2031 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2031 has 0 orthologous retrocopies within eutheria group .

---

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,