RetrogeneDB ID: retro_cjac_1516

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:46962108..46963772(-)
• Located in intron of: ENSCJAG00000020555

Retrocopy information

• Ensembl ID: ENSCJAG00000020552
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1516
ATGCTTCGGTTACCCACCGTCTTTCGCCAGATGAGACCGGTTTCCAGGGTCCTGGCTCCTCATCTCACTCGGGCTTACGC
CAAAGATGTAAAATTTGGTGCAGATGCCCGAGCCTTAATGCTTCAAGGTGTAGACCTTTTAGCCGATGCCGTAGCTGTTA
CAATGGGGCCAAAGGGAAGAACAGTGATTATTGAGCAAAGCTGGAGAAGTCCCAAAGTAACAAAAGATGGTGTGACTGTT
GCAAAGTCAATTGACTTAAAGGATAAATATAAAAATATTGGAGCTAAACTTGTTCAAGATGTTGCCAATAACACAAATGA
AGAGGCTGGGGATGGCACTACCACGGCTACTGTCTGGCACGCTCTATTGCCAAGGAAGGCTTCGAGAAGATTAGCAAAGG
TGCTAATCCAGTGGAAATCAGGAGAGGTGCGATGTTAGCTGTTGATGCTGTAATTGCCGAACTTAAAAAGCAGTCTAAAC
CTGTGACCACCCCCGAAGAAATTGCACAGGTTGCTACAATTTCTGCAAATGGAGACAAAGAAATTGGGAATATCATCTCT
GATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGATGGAAAAACACTTAATGATGAATTAGAAGTTAT
TGAAGGCATGAAGTTTGATCGAGGATATATTTCTCCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAGG
ATGCCTATGTTCTGTTGAGTGAAAAGAAAATTTCTAGTGCCCAGTCGATTGTACCTGCTCTTGAAATTGCCAATGCTCAC
CGTAAGCCTTTGGTCATAATCGCTGAAGACGTTGATGGAGAAGCTCTAAGTACACTTGTCTTGAATAGGCTAAAGGTTGG
TCTTCAGGTTGTGGCGGTCAAGGCTCCAGGGTTTGGTGACAATAGAAAGAACCAACTTAAAGATATGGCTATTGCTACTG
GTGGTGCAGTGTTTGGAGAAGAGGGATTGACCCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGGAAAGTTGGAGAG
GTCATTGTGACCAAAGATGATGCCATGCTCTTAAAAGGAAAAGGTGACAAGGCTCAAATTGAAAAACGTATTCAAGAAAT
CATTGAGCAGCTAGATGTCACAACTAGTGAATATGAAAAGGAAAAACTGAATGAACGGCTGGCAAAACTTTCAGATGGAG
TAGCTGTGCTGAAGTTTGGTGGGACAAGTGATGTTGAAGTGAATGAAAAGAAAGACAGAGTTACAGATGCCCTTAATGCT
ACAATAGCTGCTGTTGAAGAAGGCATTGTTTTGGGAGGGGGTTGTGCCCTGCTTCGGTGCATTCCAGCCTTAGACTCATT
GACTCCAGCTAATGAAGATCAAAAAATTGGTATAGAAATTATTAAAAGAACACTCAAAATTCCAGCAATGACCATTGCTA
AGAATGCAGGTGTTGAAGGATCTTTGATAGTTGAGAAAATTATGCAAAGTTCCTCAGAAGTTGGTTATGATGCTATGGCT
GGAGATTTTGTGAATATGGTGGAAAAAGGGATTATTGACCCAACAAAGGTTGTGAGAACTGCTTTATTGGATGCTGCTGG
TGTAGCCTCTCTGTTAACTACAGCAGAAGTTGTAGTCACAGAAATTCCTAAAGAAGAGAAAGAC

Alignment

ORF - retro_cjac_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.56 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
          MLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSW.S
Retrocopy MLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWRS

Parental  PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATV-LARSIAKEGFEKISKGANPVE
          PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATV.LARSIAKEGFEKISKGANPVE
Retrocopy PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATV<LARSIAKEGFEKISKGANPVE

Parental  IRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLND
          IRRG.MLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLND
Retrocopy IRRGAMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLND

Parental  ELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVD
          ELE.IEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISS.QSIVPALEIANAHRKPLVIIAEDVD
Retrocopy ELEVIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSAQSIVPALEIANAHRKPLVIIAEDVD

Parental  GEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVI
          GEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVI
Retrocopy GEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVI

Parental  VTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKD
          VTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLK.GGTSDVEVNEKKD
Retrocopy VTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKFGGTSDVEVNEKKD

Parental  RVTDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVEGSL
          RVTDALNAT.AAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVEGSL
Retrocopy RVTDALNATIAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVEGSL

Parental  IVEKIMQSSSEVGYDAMAGDFVNMVDKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD
          IVEKIMQSSSEVGYDAMAGDFVNMV.KGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD
Retrocopy IVEKIMQSSSEVGYDAMAGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD

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	0.49 RPM	61.81 RPM
SRP051959_heart	0.44 RPM	59.55 RPM
SRP051959_kidney	0.69 RPM	131.50 RPM
SRP051959_liver	0.63 RPM	191.35 RPM
SRP051959_lung	0.34 RPM	48.36 RPM
SRP051959_lymph_node	0.43 RPM	75.59 RPM
SRP051959_skeletal_muscle	0.11 RPM	48.39 RPM
SRP051959_spleen	0.40 RPM	61.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1516 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1516 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,