RetrogeneDB ID: retro_cjac_3528

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01183108.1:8691..9204(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSCJAG00000019486
• Aliases: None
• Description: zinc finger, CCHC domain containing 9 [Source:HGNC Symbol;Acc:25424]

Sequence

>retro_cjac_3528
GAAGTAAGGGAAGAAATTGCAGTTGCTTTAAAGAAAGACAGTCAATGGGAAGGAAGAAGATTAAAAAGACAAGTGGCAAA
GAAAAATGCAGTGGTGTTTCTATTGTAGAAAACCTGGTCATGGAATTGCAGATTGCCCTGCACCCTTGAAAATCAACATA
CTGGAGTATGTTACAGGTGTGGGTCCACAGAGCACGAAATAACCAAGTGTAAGGCTAAAGTAGATCCGGCTCTTGGTGAA
TTTCCTTTCACAAAATGTTTTGTTTGTGGAGAAATGGGGCACCTCTCTAGAGCTTGTCCTGATAATCCCAAAGGACTCTA
TGCTGATGGTGGTGGTTGCAAACTTTGTGGCTCTGTGAAACATTTAAAGAAAGATTGCCTGGAAAATCAGAATTCAGATC
GAATGGTCACAGTTGGTCACTGGGCAAAGGGAATGAGTACAGATTATGAAGAAATTTTGGATGCACCTAAACCACAAAAA
CCCAAAACAAAAATACCTAAAGTTGTTAATTTT

Alignment

ORF - retro_cjac_3528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.75 %
• Parental protein coverage: 64.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVREEIAVALKKDSRREGRRL-KRQAAKKNA-MVCFHCRKPGHGIADCPA-ALENQDMGTGICYRCGSTE
          EVREEIAVALKKDS..EGRRL.K....K......CF.CRKPGHGIADCPA..LENQ...TG.CYRCGSTE
Retrocopy EVREEIAVALKKDSQWEGRRL<KKTSGKEKC<QWCFYCRKPGHGIADCPA<TLENQH--TGVCYRCGSTE

Parental  HEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSVEHLKKDCPENQNSDR
          HEITKCKAKVDPALGEFPF.KCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSV.HLKKDC.ENQNSDR
Retrocopy HEITKCKAKVDPALGEFPFTKCFVCGEMGHLSRACPDNPKGLYADGGGCKLCGSVKHLKKDCLENQNSDR

Parental  MVTVGRWVKGMSADYEEILDAPKLQKPKTKIPKVVNF
          MVTVG.W.KGMS.DYEEILDAPK.QKPKTKIPKVVNF
Retrocopy MVTVGHWAKGMSTDYEEILDAPKPQKPKTKIPKVVNF

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	0.80 RPM	5.57 RPM
SRP051959_heart	0.82 RPM	10.59 RPM
SRP051959_kidney	0.51 RPM	7.94 RPM
SRP051959_liver	0.35 RPM	7.52 RPM
SRP051959_lung	0.88 RPM	8.20 RPM
SRP051959_lymph_node	1.32 RPM	8.13 RPM
SRP051959_skeletal_muscle	0.79 RPM	9.15 RPM
SRP051959_spleen	1.03 RPM	9.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3528 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528 , retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,