RetrogeneDB ID: retro_cjac_1975

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:169218187..169219837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSCJAG00000003990
• Aliases: None
• Description: None

Sequence

>retro_cjac_1975
TCCAGGGTCCTGGCTCCTCATCTCACTCGGGCTTATGCCAAAGATGTAAAATTTGGTGCAGATGCCTGAGTCTTAATGCT
TCTAGGTATGGATCTTTTAGCCGATGCCATAGCTGTTACAATGGGGCTAATAACAGTGATTATTGAGCAAAGCTGGGTAA
GTCCCAAAGTAACAAAAGATGGTGTGACTGTTGCAAAGTCCACTGACTAAAAGGATAAATATAAAAATACTGGAGCTAAC
CTTCTTCAAGATGTTACCAATAACACAAATGAAGAGGCTGGGGATGGCACTACCATGACTACTGTACTGGCACACTCTAT
TGCCAAGGAAGGCTTCAAGAAGATTAGCAAAGGTACTAATACAATGGAAATCAGGAGAGGTGTGATGTTAGCCATTGATG
CTGTAATTGTTGAACTTAAAAAGCAGTCTAAACCTGTGACCACCCCCGAAGAAATTGCACAGGTTGCTACAATTTCTGCA
AATGGAGACAAAGAAATTGGGAGTATCATCTCTGATGCTATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGA
TGGAAAAACACTGAATGATGAACTAGAAATTGTTGAAGGCATGAAGTTTGATTGAGGCTATATTTCTCCATGCTTTATTA
ATATGTCAAAAGGTCAGAAACATGAATTCCAGGATGCCTATGTTCTGTTGAGTGAAAAGAAAATTTCTAGCGTCCAGTCC
ATTGTACCTGCTCTTGAAATTGCCAGTGCTCACTGTAAGGCTTTGGTCATAATGGCTGGAGACATTGATGGAGAAGCTCT
GAGTACATTTGTCTTGAATAGGCTAAAGGTTGGTCTTCAGGTTGCGGCAGTTAAGGCTCCAGGGTTTGGTGACAACAGTA
AGAACCAGCCTAAAGATATGACTATTGCTACTGGTGATGCAGTGTTTGGTGAAGAGGGGTTGACCTTAAATCTTGAAGAT
GTTCAGCATCATGACTTTGGAAAAGTTGGGGAGGTCATTGTGACCAAAGATGATGCCAAGCTCTTAAAATAAAAAGGTAA
CAAGGCTCTAATTGAAAAACCTATTCAAGATATCATTGGGCAGCTAGATGTTACAACTAGTGAATATGAGAAGGAGAAAC
TGAATGAATGGCTGGCAAAACTTTCAGGTGGAGTAGCTGTGCTGCAGGTTGGTGGGACAAGTGTTGTTGAAATAAATAAA
AAGAAGACAGAGTTATGGATGCCCTTAACGCTACAAGAGCTGCTGTTGAATAAGGCATTGTTTTGGGAGGGAGTTTTGTC
CTGCTTTGGTACACTCCAGCCAAAGCTGGACTCTAGCTAATGAAGATCAAAAATTGGTATAGAAATTATTTAAAGAATGC
ACAAAATTCCAGCAATGACCATTGCTAAGAATGTAGGTGTTGAGGAATCTTTGATAGTTGAGAAAATTAGGCAAAGTTCC
TCAGAAGTTGGTTATGATGCTATGGCTGGAGATTTTGTGAATATGGTGGAAAAATGAATTATTGACCCAACAAAGGTTGT
GAGAACTGATTTATTGGATGCTGCTGGTGTGGCCTCTCTGTTAACTACAGCAGCAGTTGCAGTCACAGAAATTCCTAAAG
AAGAGAAGGACCCTGGAATGGGTGCAATGGGTGGAATGGGAGGTGGCATG

Alignment

ORF - retro_cjac_1975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.69 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGSPKVTKDGVTVAKSI
          SRVLAPHLTRAYAKDVKFGADA..LML.G.DLLAD..A........TVIIEQSW.SPKVTKDGVTVAKS.
Retrocopy SRVLAPHLTRAYAKDVKFGADA*VLMLLGMDLLAD--AIAVTMGLITVIIEQSWVSPKVTKDGVTVAKST

Parental  DLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEIRRGVMLAVDAVIAE
          D.KDKYKN.GA.L.QDV.NNTNEEAGDGTT..TVLA.SIAKEGF.KISKG.N..EIRRGVMLA.DAVI.E
Retrocopy D*KDKYKNTGANLLQDVTNNTNEEAGDGTTMTTVLAHSIAKEGFKKISKGTNTMEIRRGVMLAIDAVIVE

Parental  LKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYI
          LKKQSKPVTTPEEIAQVATISANGDKEIG.IISDAMKKVGRKGVITVKDGKTLNDELEI.EGMKFD.GYI
Retrocopy LKKQSKPVTTPEEIAQVATISANGDKEIGSIISDAMKKVGRKGVITVKDGKTLNDELEIVEGMKFD*GYI

Parental  SPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVLNRLKVG
          SP.FIN.SKGQK.EFQDAYVLLSEKKISSVQSIVPALEIA.AH.K.LVI.A.D.DGEALST.VLNRLKVG
Retrocopy SPCFINMSKGQKHEFQDAYVLLSEKKISSVQSIVPALEIASAHCKALVIMAGDIDGEALSTFVLNRLKVG

Parental  LQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLLKGKGDK
          LQV.AVKAPGFGDN.KNQ.KDM.IATG.AVFGEEGLTLNLEDVQ.HD.GKVGEVIVTKDDA.LLK.KG.K
Retrocopy LQVAAVKAPGFGDNSKNQPKDMTIATGDAVFGEEGLTLNLEDVQHHDFGKVGEVIVTKDDAKLLK*KGNK

Parental  AQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKK-DRVTDALNATRAAVE
          A.IEK.IQ.II.QLDVTTSEYEKEKLNE.LAKLS.GVAVL.VGGTS.VE.N.KK.DRV.DALNATRAAVE
Retrocopy ALIEKPIQDIIGQLDVTTSEYEKEKLNEWLAKLSGGVAVLQVGGTSVVEINKKK<DRVMDALNATRAAVE

Parental  EGIVLGGGCALL-RCIPALDSLTPANEDQK-IGIEIIKRTLKIPAMTIAKNAGVEGSLIVEKIMQSSSEV
          .GIVL.GG...L........S.T.ANEDQK.IGIEII.R..KIPAMTIAKN.GVE.SLIVEKI.QSSSEV
Retrocopy *GIVL-GGSFVL<ALVHSSQSWTLANEDQK<IGIEII*RMHKIPAMTIAKNVGVEESLIVEKIRQSSSEV

Parental  GYDAMAGDFVNMVDKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKDPGMGAMGGMGGGM
          GYDAMAGDFVNMV.K.IIDPTKVVRT.LLDAAGVASLLTTA.V.VTEIPKEEKD..........GGM
Retrocopy GYDAMAGDFVNMVEK*IIDPTKVVRTDLLDAAGVASLLTTAAVAVTEIPKEEKDXXXXXXXXXXGGM

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	0.04 RPM	61.81 RPM
SRP051959_heart	0.00 RPM	59.55 RPM
SRP051959_kidney	0.07 RPM	131.50 RPM
SRP051959_liver	0.09 RPM	191.35 RPM
SRP051959_lung	0.08 RPM	48.36 RPM
SRP051959_lymph_node	0.02 RPM	75.59 RPM
SRP051959_skeletal_muscle	0.04 RPM	48.39 RPM
SRP051959_spleen	0.02 RPM	61.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1975 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1975 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Bos taurus	ENSBTAG00000012586	1 retrocopy	retro_btau_988,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni	ENSCHOG00000007401	5 retrocopies	retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975 , retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus	ENSDNOG00000013226	3 retrocopies	retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens	ENSG00000144381	7 retrocopies	retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla	ENSGGOG00000008267	6 retrocopies	retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus	ENSMUSG00000025980	5 retrocopies	retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys	ENSNLEG00000006874	7 retrocopies	retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii	ENSPPYG00000013046	5 retrocopies	retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Pteropus vampyrus	ENSPVAG00000008306	1 retrocopy	retro_pvam_250,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus	ENSSTOG00000028470	1 retrocopy	retro_itri_224,
Tarsius syrichta	ENSTSYG00000000513	6 retrocopies	retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Tursiops truncatus	ENSTTRG00000003417	3 retrocopies	retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,