RetrogeneDB ID: retro_cjac_1639

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:32624369..32625039(+)
• Located in intron of: ENSCJAG00000009018

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSCJAG00000016488
• Aliases: None
• Description: forty-two-three domain containing 1 [Source:HGNC Symbol;Acc:25407]

Sequence

>retro_cjac_1639
CAGCGATTTAAGATGAGAATACAATGGGTATTCCAACAGAATTCTGGTTTTGGTAAAACCAGTGTAAGCTGTGGAGGAAG
AGTAATGCCTGGAAAGAGACATCCTCATGGATAATCATTGGCCTTGCAGTTAGGAAATCATCTGGAATTGGAAAAGGAAT
TAGTCCCATGAATTGTCCACATGTAAGTAACAAGAATACAAAACAATATTTTCCAGTGTTAAAAAGAAAGGCAAGTCTTC
TGAAACAAAATGAACTATGCAGGACACCAACTGCAGTTCTCAAAGAGACCTAACCAGCTAAACAGAAAAAATAACATTAA
GGCTAATTTTACCAGGAAAGGAAATAGATTAAGCCATCAGAAAGACACTTCACAGGTAACTTTTCTTTTCAGAAGAGGCC
TGAAGAATGTTCAGGCCCAGTTGAACACAGAACAGCTACTAGATGATGTAGCAGCGAAGAGAACTAGTCAATGCTGGACT
TCCATCACAAATGCAGGAATTTGACTGTATCTACTGACAACCCCGGAACAGTACAATGCCCAGTAACTCAGAAACCATAA
TTAATTCATACTGCTTTACCTTTATTCTTTAAAAACATCAGCAAGAGAATGTAAAGAAAGTTCCCACAGGTGTTCCCCTA
CAATTTGACATAAATAGTGTTGGAAAACAG

Alignment

ORF - retro_cjac_1639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.93 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RQFRMRVRWGIQQNSGFGKTSLNRRGRVMPGKRRPNG-VITGLAARKTTGIRKGISPMNRPPLSDKNIER
          ..F.MR..W..QQNSGFGKTS....GRVMPGKR.P.G..I.GLA.RK..GI.KGISPMN.P..S.KN...
Retrocopy QRFKMRIQWVFQQNSGFGKTSVSCGGRVMPGKRHPHG<IIIGLAVRKSSGIGKGISPMNCPHVSNKNTKQ

Parental  YFPVLKRKANLLRQNEGQRKPVAVL-KRPNQLNRKNSIPANFTRSGNKLNHQKDTRQATFLFRRGLK-VQ
          YFPVLKRKA.LL.QNE..R.P.AVL.KRPNQLNRKN.I.ANFTR.GN.L.HQKDT.Q.TFLFRRGLK.VQ
Retrocopy YFPVLKRKASLLKQNELCRTPTAVL>KRPNQLNRKNNIKANFTRKGNRLSHQKDTSQVTFLFRRGLKNVQ

Parental  AQLNTEQLLDDVVAKRTRQWRTSTTNGGI-LTVSIDNPGAVQCPVTPKPRLTRTAVPSF-LSKREQNDVK
          AQLNTEQLLDDV.AKRT.Q..TS.TN.GI.LTVS.DNPG.VQCPVT.KP.L..TA.P.F.L.K..Q..VK
Retrocopy AQLNTEQLLDDVAAKRTSQCWTSITNAGI<LTVSTDNPGTVQCPVTQKP*LIHTALPLF<L*KHQQENVK

Parental  KVPKGVPLQFDINSVGKQ
          KVP.GVPLQFDINSVGKQ
Retrocopy KVPTGVPLQFDINSVGKQ

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	0.51 RPM	43.29 RPM
SRP051959_heart	0.37 RPM	71.35 RPM
SRP051959_kidney	0.24 RPM	43.66 RPM
SRP051959_liver	0.35 RPM	25.49 RPM
SRP051959_lung	0.46 RPM	42.99 RPM
SRP051959_lymph_node	0.75 RPM	43.58 RPM
SRP051959_skeletal_muscle	0.20 RPM	67.37 RPM
SRP051959_spleen	0.32 RPM	44.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1639 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1639 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_476
Pan troglodytes	retro_ptro_357
Gorilla gorilla	retro_ggor_450
Pongo abelii	retro_pabe_258
Macaca mulatta	retro_mmul_577

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639 , retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,