RetrogeneDB ID: retro_cjac_3209

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:37250527..37251123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSCJAG00000037305
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_cjac_3209
GGGCCAGAACTGTTGCTTGACTCCAACATCCCCCTCTAGGTGGTTCTATCCATTGTAATTATCACTTTCTTCATAGGCGT
GATCCACCACTATGTGTTCATCCTGCTGCAGAGCGATAAGAAGCCCACCTAGGAATGAGTGTCTGACAGTCAAGTCCTAA
TTCAAAGCAGAGTCCTCAGGGAAAATGGAAAACACATTCCCAAACAGTCTTTCTCAACATGAAAATATTACTTCAACAAG
CCAGAGGATGGAGTTAAAAAAAAAAAAGGAAGGTAGTGCCACCTTCTCCTGTGACTGATCCTACTATGCTGACAGACATG
ATAAAAGCAATGTAACAAATGTTATTCCTATGATTTTTATTGGTGGATGGATCAACATGACATTCTCAGGCTTTGTCACA
ACCAAAGTCCCATTTCCCCTGACCCTCCGTTTTTCAGCCTATGTTACAGCAAGGAATTGAACTACTCGCATTACATGCAT
CCTGGGTGAGTTCTGCATCCAGGTATTTCCTCAATGTATTTGGGCTTCTGCGCATTTACTCTCTGATGCTAGGCCAAGAT
AATGCCACTGACCAATCATGAATGATGCAAAAGCAG

Alignment

ORF - retro_cjac_3209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.8 %
• Parental protein coverage: 76.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRVLRENGKYIPKQS
          GPELLLDSNI.L.VVL.IVIITFF.G.I.HYV.ILLQSDKK.T.E.VSDSQVLI.SRVLRENGK.IPKQS
Retrocopy GPELLLDSNIPL*VVLSIVIITFFIGVIHHYVFILLQSDKKPT*E*VSDSQVLIQSRVLRENGKHIPKQS

Parental  FLTRKYYFNNPEDGFF-KKTKRKVVPPSPMTDPTMLTDMM-KGNVTNVLPMILIGGWINMTFSGFVTTKV
          F.T.KYYFN.PEDG...KK....V.P.SP.TDPTMLTDM..K.NVTNV.PMI.IGGWINMTFSGFVTTKV
Retrocopy FST*KYYFNKPEDGVK<KKKRKVVPP-SPVTDPTMLTDMI<KSNVTNVIPMIFIGGWINMTFSGFVTTKV

Parental  PFPLTLR-FKPMLQQGIELLTLDASWVSSASWYFLNVFGLRSIYSLILGQDNAADQSRMMQEQ
          PFPLTLR.F.PMLQQGIELL.L.ASWVSSAS.YFLNVFGL..IYSL.LGQDNA.DQS.MMQ.Q
Retrocopy PFPLTLR>FQPMLQQGIELLALHASWVSSASRYFLNVFGLLRIYSLMLGQDNATDQS*MMQKQ

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	10.29 RPM
SRP051959_heart	0.00 RPM	8.68 RPM
SRP051959_kidney	0.00 RPM	14.91 RPM
SRP051959_liver	0.00 RPM	17.29 RPM
SRP051959_lung	0.00 RPM	9.81 RPM
SRP051959_lymph_node	0.00 RPM	8.40 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.58 RPM
SRP051959_spleen	0.00 RPM	9.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3209 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3209 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209 ,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,