RetrogeneDB ID: retro_cjac_2289

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:148874546..148874966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN17
• Ensembl ID: ENSCJAG00000007278
• Aliases: None
• Description: tetraspanin 17 [Source:HGNC Symbol;Acc:13594]

Sequence

>retro_cjac_2289
TGGCCATTTGTGGTTGTTGCAGGCACCATGTTGGTGCCAGGCTCTGCTGGCTGTATCAGGACCCTTCAGGAAAACACCTT
TCTGTTCAAGTTTTTCTCCATATTCTTTGGCCTGATCTTCTTCCTGGAGCTGGCAATGGGGATCCTGGTCTTTGTCTTCA
AAGACTGAATTCAAGACCAGCTCAACCACTTTAGCAACCACAATGTCAAGACCTACCATGACAACATTGACCTCCAGAAG
CTCATTGACTTTGCTTAGGAATATTGGTCTTGCTGCAGAGCCCAAGGGCCCAGTGACTGGAACCTCAGCATCTACTTCAA
CAGCTCTGACTTGAATCCAAGATGGGAGCACTGAGCATTACTTTTCTCTTGCTGCATCAGAGGCCCTGCAGAAAATGCCC
TCAGCACCCAGTATGGCTAT

Alignment

ORF - retro_cjac_2289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.29 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLFVVVGGVMSVLGFAGCIGALRENTFLLKFFSMFLGLIFFLELATGILAFVFKDWIRDQLNLFINNNVK
          W.FVVV.G.M.V.G.AGCI..L.ENTFL.KFFS.F.GLIFFLELA.GIL.FVFKD.I.DQLN.F.N.NVK
Retrocopy WPFVVVAGTMLVPGSAGCIRTLQENTFLFKFFSIFFGLIFFLELAMGILVFVFKD*IQDQLNHFSNHNVK

Parental  AYRDDIDLQNLIDFAQEYWSCCGARGPNDWNLNIYFNCTDLNPSRERCGVPFSCCLRDPAEDVLNTQCGY
          .Y.D.IDLQ.LIDFA.EYWSCC.A.GP.DWNL.IYFN..DLNP..E.....FSCC.R.PAE..L.TQ.GY
Retrocopy TYHDNIDLQKLIDFA*EYWSCCRAQGPSDWNLSIYFNSSDLNPRWEH*ALLFSCCIRGPAENALSTQYGY

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	20.08 RPM
SRP051959_heart	0.00 RPM	10.28 RPM
SRP051959_kidney	0.00 RPM	10.21 RPM
SRP051959_liver	0.00 RPM	7.91 RPM
SRP051959_lung	0.00 RPM	10.75 RPM
SRP051959_lymph_node	0.00 RPM	9.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.87 RPM
SRP051959_spleen	0.00 RPM	6.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2289 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007218	2 retrocopies	retro_amel_1365, retro_amel_979,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585, retro_cfam_704,
Callithrix jacchus	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289 ,
Callithrix jacchus	ENSCJAG00000016486	1 retrocopy	retro_cjac_4116,
Equus caballus	ENSECAG00000022322	1 retrocopy	retro_ecab_554,
Felis catus	ENSFCAG00000007803	1 retrocopy	retro_fcat_1133,
Mustela putorius furo	ENSMPUG00000012505	1 retrocopy	retro_mputfur_428,