RetrogeneDB ID: retro_cjac_801

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:86282660..86283440(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021879
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSCJAG00000010325
• Aliases: None
• Description: None

Sequence

>retro_cjac_801
CCCTGCTCGTGCGCCTGGTACTTCTCGCTGCCCGAGCTTTTCCAGGGCCCCGTCTACCTCTACTACGAGCTGACCAACTT
CTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACGAGCAGCTGAGCGGAATGCCCAGCGCGCTGCGCCACCCGG
CCAACGAGTGCGCCCCCTACCAGCGCAGCGCAGCCGGCCTGCCCATCGCGCCCTGCGGCGCCATCGCCAACAGCCTCTTC
AACGACTCCTTCTCGCTGTGGCACCAGCGCCAGTCTGGCGGGCCCTACGTCGAGGTGCCGCTCGACCGCTCCGGCATCGC
CTGGTGGACTGACTACCACGTCAAGTTCCGCAACCCGCCGCTGGTAAACGGCAGCCTGGCGCTGGCCTTCCAAGGCACGG
TGCCTCCGCCAAACTGGCGCCGGCCGGTCTACGAGCTCAGCCCCGACCCCAACAACACCGGCTTCATCAACCAGGACTTC
GTGGTGTGGATGCGCACGGCGGCGCTGCCCACGTTTCGCAAGCTGTACGCGCGCATCCGCCAGGGCAACTACTCTGCCGG
GCTGCCGCGGGGCGCCTACCGCGTCAATATTACCTACAACTACCCGGTGCGCGCGTTCGGCGGCCACAAGCTCCTCATCT
TCAGCAGCATCTCGTGGATGGGCGGCAAGAACCCCTTCCTGGGCATCGCGTACCTGGTCGTCGGCTCCCTCTGCATCCTC
ACTGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGGACGATGATGACGAC

Alignment

ORF - retro_cjac_801 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.17 %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PCICTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNE-DKPIA
          PC.C...F.L...F.G.V..YY.L.NFYQN.RRY..SRDD.QL.G..SAL..P..EC.PY.R.....PIA
Retrocopy PCSCAWYFSLPELFQGPVYLYYELTNFYQNNRRYGVSRDDEQLSGMPSALRHPANECAPYQRSAAGLPIA

Parental  PCGAIANSMFNDTLELFLIGNDSYP-MPIALKKKGIAWWTDKNVKFRNPPGGDNNLEERFKGTTKPVNWL
          PCGAIANS.FND...L........P.....L...GIAWWTD..VKFRNPP.....L...F.GT..P.NW.
Retrocopy PCGAIANSLFNDSFSLWHQRQSGGPYVEVPLDRSGIAWWTDYHVKFRNPPLVNGSLALAFQGTVPPPNWR

Parental  KPVYMLDSDQDNNGFINEDFIVWMRTAALPTFRKLYRLIERKSDLHPTLPAGRYYLNITYNYPVHYFDGR
          .PVY.L..D..N.GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..NITYNYPV..F.G.
Retrocopy RPVYELSPDPNNTGFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGAYRVNITYNYPVRAFGGH

Parental  KRMILSTISWMGGKNPFLGIAYIAVGSISFLLGVVLLVINHKYRNSSNTAD
          K..I.S.ISWMGGKNPFLGIAY..VGS...L.G.V.LV....Y.......D
Retrocopy KLLIFSSISWMGGKNPFLGIAYLVVGSLCILTGFVMLVVYIRYQDQDDDDD

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	1.66 RPM	59.68 RPM
SRP051959_heart	2.05 RPM	60.11 RPM
SRP051959_kidney	2.73 RPM	85.68 RPM
SRP051959_liver	1.88 RPM	74.60 RPM
SRP051959_lung	1.69 RPM	81.34 RPM
SRP051959_lymph_node	0.14 RPM	58.35 RPM
SRP051959_skeletal_muscle	1.05 RPM	44.62 RPM
SRP051959_spleen	0.11 RPM	92.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_801 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_801 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801 ,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,