RetrogeneDB ID: retro_cjac_2908

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:85575834..85576427(+)
• Located in intron of: ENSCJAG00000021555

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBSCR22
• Ensembl ID: ENSCJAG00000016799
• Aliases: None
• Description: None

Sequence

>retro_cjac_2908
GAGCATGGCAGACCCCTGGAGCTGTTTTATGACAAGAAAAAAAAAAAAGCCTGGAAATACATTCCCAACTCACAGATGCT
TTGATTTCCAGATCAGGATGGCTGGGCGAGCATTGGAGCTTCTTTATCTGCCAGAGAATAAGCCCTGTTACCTGCTGGAT
ACTGGCTGTGGCACTGGGCTGAGTGAAGGTTCTCTCTCAGATGAAGGGCACTATTGGGTGGGCCTGGATATCAGCCCTGC
CATGCAGTATAAGGCCGTGGACTGAGATATAGAGGGAGACCTGCTTTTGGGGGACATGGGCCAGGGCATCCATTTCAAGC
TAGGCATATCTGATGGTTGCAGCAGCATTTCTGCTGTGCAGTGGTTCTGTAATGCTAACAAGAAATCTGAATATCCTGTC
AAGCACCTGTACTGCTTTTTAGCTTCTCTTTTTTCTGTTCTTGTCCAGGGATCCCAAGCTGTCTTGCAGCTATAACCTGA
GAACTCAGAGCTTGTAGGGGCTGATCACAACACAGGCGACAAAGGCGGGCTCCTCCGGTGGCATGGTGGTAGACTACCCC
GCCAGTGCCAAAGGAAAGAAGTTCTACCTCTGC

Alignment

ORF - retro_cjac_2908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.64 %
• Parental protein coverage: 68.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EHGGPPELFYDKKEAR--KYVSNSRMI-EIQTRMAGRALELLCLPRNKPCYLLDIGCGTGLSGGYLSNEG
          EHG.P.ELFYDKK.....KY..NS.M....Q.RMAGRALELL.LP.NKPCYLLD.GCGTGLS.G.LS.EG
Retrocopy EHGRPLELFYDKKKKKAWKYIPNSQML>DFQIRMAGRALELLYLPENKPCYLLDTGCGTGLSEGSLSDEG

Parental  HCWVGLDISPAMLDVDEAVDREVEGDLLLGDMGQGIPFKPGTFDGCISISAVQWLCNANKKSENPVKRLY
          H.WVGLDISPAM.....AVD...EGDLLLGDMGQGI.FK.G..DGC.SISAVQW.CNANKKSE.PVK.LY
Retrocopy HYWVGLDISPAMQY--KAVD*DIEGDLLLGDMGQGIHFKLGISDGCSSISAVQWFCNANKKSEYPVKHLY

Parental  CFFASLFSVLVRGSRAVLQLYPENSEQL-ELITAQAMRAGFSGGVVVDYPNSARAKEAFLC
          CF.ASLFSVLV.GS.AVLQL.PENSE....LIT.QA..AG.SGG.VVDYP.SA..K...LC
Retrocopy CFLASLFSVLVQGSQAVLQL*PENSELV>GLITTQATKAGSSGGMVVDYPASAKGKKFYLC

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	0.38 RPM	8.81 RPM
SRP051959_heart	0.61 RPM	5.51 RPM
SRP051959_kidney	0.95 RPM	13.82 RPM
SRP051959_liver	0.39 RPM	7.04 RPM
SRP051959_lung	0.54 RPM	6.72 RPM
SRP051959_lymph_node	0.84 RPM	5.27 RPM
SRP051959_skeletal_muscle	0.61 RPM	9.26 RPM
SRP051959_spleen	0.76 RPM	6.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2908 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2908 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016799	1 retrocopy	retro_cjac_2908 ,
Echinops telfairi	ENSETEG00000008874	1 retrocopy	retro_etel_1185,
Oryctolagus cuniculus	ENSOCUG00000017297	1 retrocopy	retro_ocun_758,
Tupaia belangeri	ENSTBEG00000007038	1 retrocopy	retro_tbel_4216,