RetrogeneDB ID: retro_cjac_4178

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65324701..65325328(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD10
• Ensembl ID: ENSCJAG00000002763
• Aliases: None
• Description: programmed cell death 10 [Source:HGNC Symbol;Acc:8761]

Sequence

>retro_cjac_4178
ATGAGGATGACAATGGAAGAGATAAAGAATGAAGCTGAGATCACATCCATGGTTTCTATGCCCCTCTATCCAGTCATGTA
TCCTGTATTTAATGAGTTAGAATGAGTAAATCTGTCTGTAGCTCAGACACTGAGAGCTGCTTTCATTAAGGCTGAAAAAA
AATTCAGGTCTCACACAAGACATCATTATGAAAATTTTAGAGAAAAAAGTGTAGAAATTAACTTCATGGATTCCTTTCTT
TGTATGGCAGCTGATGATGTAGAAGAGCATATGATTGAGTAACCAGAGCCAGAATCCTGAGACCTAAATGAAAAGTCATG
AGCACTTAAATTTTCAGTAATATCCCAGATGAGATCAATGACAGTGAGGTTTCTGCAGACAATCAAGGATATAGCTAGTG
CAATAAAAGAACTTCTTGATACAGTGAATAATGCCTTCAAGAAATATCAATACCAGAACCGCAGGGCACTTGAACACCAA
AAGAAAGAATTTATGAAGTACTCCAAAAGTTTCAGTGATACTCTGAAAACATATTTTAAAGATGGCAAGGCAATTAATGT
GTTCATAAGTGCCAACTGACTAATTAATTAAACCAACTTAATACTTCCGACCTTCAAAGCTGTGGCC

Alignment

ORF - retro_cjac_4178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRMTMEEMKNEAETTSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK
          MRMTMEE.KNEAE.TSMVSMPLY.VMYPVFNELE.VNLS.AQTLRAAFIKAEK.....T........E.K
Retrocopy MRMTMEEIKNEAEITSMVSMPLYPVMYPVFNELE*VNLSVAQTLRAAFIKAEKKFRSHTRHHYENFRE-K

Parental  SVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE
          SVE.NF..S.L.MAADDVEE.MIE.PEPE..DLNEK..ALK...S.I.......VRFLQTIKDIASAIKE
Retrocopy SVEINFMDSFLCMAADDVEEHMIE*PEPES*DLNEKS*ALK--FSVISQMRSMTVRFLQTIKDIASAIKE

Parental  LLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT
          LLDTVNN.FKKYQYQNRRALEHQKKEF.KYSKSFSDTLKTYFKDGKAINVFISAN.LI..TNLIL.TFK.
Retrocopy LLDTVNNAFKKYQYQNRRALEHQKKEFMKYSKSFSDTLKTYFKDGKAINVFISAN*LIN*TNLILPTFKA

Parental  VA
          VA
Retrocopy VA

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	0.00 RPM	28.02 RPM
SRP051959_heart	0.00 RPM	13.96 RPM
SRP051959_kidney	0.02 RPM	23.65 RPM
SRP051959_liver	0.02 RPM	15.73 RPM
SRP051959_lung	0.03 RPM	22.56 RPM
SRP051959_lymph_node	0.00 RPM	25.34 RPM
SRP051959_skeletal_muscle	0.11 RPM	11.20 RPM
SRP051959_spleen	0.04 RPM	25.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4178 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002181	1 retrocopy	retro_amel_420,
Bos taurus	ENSBTAG00000031709	2 retrocopies	retro_btau_1623, retro_btau_713,
Canis familiaris	ENSCAFG00000014569	2 retrocopies	retro_cfam_1988, retro_cfam_687,
Callithrix jacchus	ENSCJAG00000002763	2 retrocopies	retro_cjac_1442, retro_cjac_4178 ,
Dasypus novemcinctus	ENSDNOG00000015854	1 retrocopy	retro_dnov_351,
Homo sapiens	ENSG00000114209	1 retrocopy	retro_hsap_3953,
Gorilla gorilla	ENSGGOG00000008621	1 retrocopy	retro_ggor_2656,
Loxodonta africana	ENSLAFG00000006823	1 retrocopy	retro_lafr_409,
Microcebus murinus	ENSMICG00000007004	1 retrocopy	retro_mmur_1008,
Myotis lucifugus	ENSMLUG00000016978	1 retrocopy	retro_mluc_1331,
Macaca mulatta	ENSMMUG00000005938	2 retrocopies	retro_mmul_1090, retro_mmul_2288,
Mustela putorius furo	ENSMPUG00000017075	1 retrocopy	retro_mputfur_298,
Mus musculus	ENSMUSG00000027835	1 retrocopy	retro_mmus_2113,
Nomascus leucogenys	ENSNLEG00000004874	1 retrocopy	retro_nleu_532,
Otolemur garnettii	ENSOGAG00000013887	1 retrocopy	retro_ogar_540,
Oreochromis niloticus	ENSONIG00000005553	1 retrocopy	retro_onil_40,
Procavia capensis	ENSPCAG00000010385	1 retrocopy	retro_pcap_283,
Pongo abelii	ENSPPYG00000029750	1 retrocopy	retro_pabe_3257,
Pan troglodytes	ENSPTRG00000015598	1 retrocopy	retro_ptro_2683,
Sarcophilus harrisii	ENSSHAG00000005443	1 retrocopy	retro_shar_414,
Ictidomys tridecemlineatus	ENSSTOG00000028442	3 retrocopies	retro_itri_1208, retro_itri_1377, retro_itri_322,
Tupaia belangeri	ENSTBEG00000000240	9 retrocopies	retro_tbel_1498, retro_tbel_1690, retro_tbel_2223, retro_tbel_2903, retro_tbel_3430, retro_tbel_3898, retro_tbel_3900, retro_tbel_4532, retro_tbel_95,
Tarsius syrichta	ENSTSYG00000000708	1 retrocopy	retro_tsyr_1786,
Tursiops truncatus	ENSTTRG00000016315	1 retrocopy	retro_ttru_635,