RetrogeneDB ID: retro_cjac_2338

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:53529364..53530155(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A20
• Ensembl ID: ENSCJAG00000003285
• Aliases: None
• Description: solute carrier family 25 (carnitine/acylcarnitine translocase), member 20 [Source:HGNC Symbol;Acc:1421]

Sequence

>retro_cjac_2338
ATGGCCAACCCACCAAAGCCCATCAGCCCGCTCGAGAACCTGCTGGCTAGAGGCTTTGGTGCCTTGTGCCTGGTGTTCAT
GGGGCACCCTCTGGACACTGCCAAGGTCCAACTGCAGACACAACCACTGAGTTAGTCAGGACAGCCTCCCCTGTACTCTG
GGATCTTTGACAGTCTCCCGATAACTCTTAGACAGGGCACCATGGAGCTGTATCAAGGAATGGCTGCCCCTATCATCGGG
GTCACCTCCATGTTTGCTGTGTGCTTCTCTGGGTTTGGTTTGGGGAAGAAACTACAACAGAAACACCCAGAGGATATGCT
CAGATATCCCCCGCTATTTGCAGCTGGGATGTTATCTGGTACATGGACCACAGGCATCATGATCCCTGGAGAACCCATCA
AGTGCTTGTTACCGTTTCAGGCTTCTTCAGGGGAAACCACGTACACTGGTACCTTGAACTATGCAAAGAAGCTGTACCAT
GAGTTTGGGATCCAAGGCATCTATGAAGGGACTGTGCTTACCCTTATGTGAGATGTCCCAGCTAGTGGAATATATTTCAT
GACATATGAATAACTAAAAAATATCTTCACTCCGGAGGGAAAGAGGGTCAGTGAGCTCAGTGTGCCTTGAATCCTGGTGG
CTGGGGCATAGCAGGAATCTTCAACTGGGCTGTGGCAGTCCCCCAAGATGTGCTCAAGTCTCCCTTCCAGACTGAATCTC
CTAGGAAATATCCTAACAGTTCTGTAGATGTGCTGAGGGAGATAATCTGGGATGAAGGAAGCACGTCCTTG

Alignment

ORF - retro_cjac_2338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.82 %
• Parental protein coverage: 88.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQPKPISPLKNLLAGGFGGVCLVFVGHPLDTVKVRLQTQPPSLPGQPPMYSGTFDCFRKTLIREGIMG
          MA..PKPISPL.NLLA.GFG..CLVF.GHPLDT.KV.LQTQP.S..GQPP.YSG.FD....TL.R.G.M.
Retrocopy MANPPKPISPLENLLARGFGALCLVFMGHPLDTAKVQLQTQPLS*SGQPPLYSGIFDSLPITL-RQGTME

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKRLQQKHPEDVLSYPQLFAAGMLSGVFTTGIMTPGERIKCLLQI
          LY.GMAAPIIGVT.MFAVCF.GFGLGK.LQQKHPED.L.YP.LFAAGMLSG..TTGIM.PGE.IKCLL..
Retrocopy LYQGMAAPIIGVTSMFAVCFSGFGLGKKLQQKHPEDMLRYPPLFAAGMLSGTWTTGIMIPGEPIKCLLPF

Parental  QASSGETKYTGTLDCAKKLYQEFGIRGIYKGTVLTLMRDVPASGMYFMTYEWLKNIFTPEGKRVSELSAP
          QASSGET.YTGTL..AKKLY.EFGI.GIY.GTVLTLM.DVPASG.YFMTYE.LKNIFTPEGKRVSELS.P
Retrocopy QASSGETTYTGTLNYAKKLYHEFGIQGIYEGTVLTLM*DVPASGIYFMTYE*LKNIFTPEGKRVSELSVP

Parental  RILVAG-GIAGIFNWAVAIPPDVLKSRFQTAPPGKYPNGFRDVLRELIRDEGITSL
          .ILVAG.GIAGIFNWAVA.P.DVLKS.FQT..P.KYPN...DVLRE.I.DEG.TSL
Retrocopy *ILVAG<GIAGIFNWAVAVPQDVLKSPFQTESPRKYPNSSVDVLREIIWDEGSTSL

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	0.33 RPM	6.15 RPM
SRP051959_heart	0.21 RPM	10.68 RPM
SRP051959_kidney	0.16 RPM	12.56 RPM
SRP051959_liver	0.04 RPM	12.35 RPM
SRP051959_lung	0.24 RPM	7.40 RPM
SRP051959_lymph_node	0.55 RPM	7.47 RPM
SRP051959_skeletal_muscle	0.09 RPM	6.73 RPM
SRP051959_spleen	0.38 RPM	9.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2338 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2338 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3469
Pan troglodytes	retro_ptro_2352
Gorilla gorilla	retro_ggor_2341
Pongo abelii	retro_pabe_2865
Macaca mulatta	retro_mmul_1764

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338 ,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,