RetrogeneDB ID: retro_cjac_3220

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:56593864..56594383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSCJAG00000001584
• Aliases: None
• Description: mitochondrial ribosomal protein L40 [Source:HGNC Symbol;Acc:14491]

Sequence

>retro_cjac_3220
CAGTGAGCTTCAGTGTTGTCATCCTAGGAACTCGTTCCTGTGACAGCAGAAACTTTTTGAGAGCAGAAGGTGGATCCTAA
AAAAGACAAGCAGGAAAGGGCTGCTTGAAAAATAAGATGTGAAAACAGGAAAAGGCTAGCCAAGAGTTCATTCTTGTTGC
AGCTTTTATTACCCTTGTGAGGTTCCTGGATAAAGTAAGCCAGAGGCCTCAGGTGGAGCTCTCCTTGGAGGAGAGTGAGT
GGAGAGCTCTGCTTCTCAGGAGTGGTCCCTGTACAAGCAGCAAGAGCACGTGATGGACTGGGACACCATCAGGGCCGTGC
TGGAGGCTCAGCAGGAAGCTCTATAGGAGCTGCCACTCAGTCCCCTGAGTTCCCCACTGAGGCCATCAGGTGAGACCACA
GCATGTTCCCCTTTGAGAGAGATGGTCCAGATTACACACTACAGGTCTCTAACTACCAGCCCCCTAAAGGCAGGTACAAT
GACATCACCAAGGTGTACACACAGGTAGAGCTGAAGAGA

Alignment

ORF - retro_cjac_3220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.92 %
• Parental protein coverage: 84.54 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QRASLLSFWEVIPMRSEPVRKKKKVDPKKD-QAVKDRLKRRIRKLEKASQELIPIEDFITPIKFLDKTRQ
          Q.AS.LS..E..P...E.....K.VDPKKD.QA.K..LK....K.EKASQE.I....FIT...FLDK..Q
Retrocopy Q*ASVLSS*ELVPVTAETF*EQK-VDPKKD<QAGKGCLKNKM*KQEKASQEFILVAAFITLVRFLDKVSQ

Parental  RPQVELSFEETERRALLLK-KWSLYKQQEHEMERDTIRAMLEAQQEALEELRL-ESPKLHAEAVKRDSNL
          RPQVELS.EE.E.RALLL...WSLYKQQEH.M..DTIRA.LEAQQEAL.EL.L..SP....EA...D...
Retrocopy RPQVELSLEESEWRALLLR<EWSLYKQQEHVMDWDTIRAVLEAQQEAL*ELPL<QSPEFPTEAIR*DHSM

Parental  FPFEREGPHYTPPIPNYQPPEGRYNDITKVYTQVEFKR
          FPFER.GP.YT....NYQPP.GRYNDITKVYTQVE.KR
Retrocopy FPFERDGPDYTLQVSNYQPPKGRYNDITKVYTQVELKR

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	5.15 RPM
SRP051959_heart	0.00 RPM	17.52 RPM
SRP051959_kidney	0.00 RPM	7.50 RPM
SRP051959_liver	0.02 RPM	12.39 RPM
SRP051959_lung	0.02 RPM	5.27 RPM
SRP051959_lymph_node	0.00 RPM	5.82 RPM
SRP051959_skeletal_muscle	0.02 RPM	16.97 RPM
SRP051959_spleen	0.00 RPM	6.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3220 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3220 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1020
Gorilla gorilla	retro_ggor_807
Pongo abelii	retro_pabe_857

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220 ,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,