RetrogeneDB ID: retro_cjac_2475

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:128997733..128998919(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSCJAG00000035699
• Aliases: None
• Description: None

Sequence

>retro_cjac_2475
GGGGACATCTATGAGAGGGCAAATACCACCTCTCTAAGGAATGCCATGGCAGCATGTCACAGTGTCCAGAGAGCCCTAGA
ACTGGATCATAAAAATGCTCAGGCCCAGCAAGAGTTCAAAAATTCTACTGCAGTCATGGAATAGGAGAAAATAGCAGAAA
CAGATTTTGAGAAGCAAGATTTCGGAAAGTAGTTTTCTGCATGGACCATGCTCTAGAATTTGCCCCTGCCTGCCATCTCT
TCAAAATCTTCAAGGCAGAATGTTTCACATTGCTGGGTTGTTATTCAGAAGCTCAGTCTGTGGCTAGTGACATTCTACGA
ATGGATTCCACCAGTGCAGATGCTCTGTATGTACGAGGTCTTTGCCTTTATTACACAGATTGTATCGAGAAGGCAGTTCA
ATTTTTTGCACAGGCTCTCAGGATGGCCCCTGACCATGAGAAGACCTGCATTGCCTGCAGAAATGCCAAAGCACTTAAAG
CAAAGAAAGAAGATGGAAATAAAGCATTGAAGGAAGGAAATTACAAACTAGCATATGAACTGTACACAGAAGCCCTGGGG
ATAGACCCCAACAATATAAAAACAAATGCAAAACTCTACTGTAATCGGGGTACTGTTAATTCCAAGCTTAGGAAACTAGA
TGATGCAATAGAAGACTTCACCAATGCAGTGAAGCTTGATAACACTTACATAAAAGCCTACTTGAGAAGAGCTCAGTGTT
ACATGGACACAGAACAGTATGAAGAAGCAGTACGAGACTGAAAAAGTGTATCAGATGGAAAAAACAAAAGAACACAAACA
GCTCCTAAAAAATGCAAAGTTGGAACTGAAGAAGAGTAAGAGGGAAGATTACTACAAAATTCTGGGAGTGGACAAGAATG
CCTCTGAGGACGAGATCAAGAAAGCTTATCGGAAATGGGCCTTGATGCACCATCCAGATCAGCATAGTGGAGCCAGTGCT
GAGGAGGAGGAGGAGGAGGAGAAGCTCATGGGAGTTGGAGAAGCCTTTACCATCCTCTCTGATGCCAAGAAAAAAAACTC
GCTATGGCAGTGGACAGGACCTGGATGAGGAGGGCCTGTATATGGGTGATTCTGATGCAAACAATATCTTCAAGGCGTTC
TTCAGCAGTCCTGCGGGCTTCAGCTTTGAAGCATCTGGTCCAGGGAATTTCTTTTTTCAGTTTGGC

Alignment

ORF - retro_cjac_2475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.79 %
• Parental protein coverage: 90.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDF-RKVVFCMD
          G...E.....SL.NAMAAC.S.QRALELDHKNAQAQQEFKN..AVME.EKIAETDFEK.DF.RKVVFCMD
Retrocopy GDIYERANTTSLRNAMAACHSVQRALELDHKNAQAQQEFKNSTAVME*EKIAETDFEKQDF<RKVVFCMD

Parental  RALEFAPACHRFKILKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKAVQFFVQA
          .ALEFAPACH.FKI.KAEC...LG.Y.EAQSVASDILRMDST.ADALYVRGLCLYY.DCIEKAVQFF.QA
Retrocopy HALEFAPACHLFKIFKAECFTLLGCYSEAQSVASDILRMDSTSADALYVRGLCLYYTDCIEKAVQFFAQA

Parental  LRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSK
          LRMAPDHEK.CIACRNAKALKAKKEDGNKA.KEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSK
Retrocopy LRMAPDHEKTCIACRNAKALKAKKEDGNKALKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSK

Parental  LRKLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEEAVRD-YEKVYQTEKTK-EHKQLLKNAQLEL
          LRKLDDAIED.TNAVKLD.TYIKAYLRRAQCYMDTEQYEEAVRD...K.....K.K.EHKQLLKNA.LEL
Retrocopy LRKLDDAIEDFTNAVKLDNTYIKAYLRRAQCYMDTEQYEEAVRD<LKKCIRWKKQK<EHKQLLKNAKLEL

Parental  KKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEVGEAFTILSD-PKK
          KKSKR.DYYKILGVDKNASEDEIKKAYRK.ALMHHPD.HSGASA........K...VGEAFTILSD.P.K
Retrocopy KKSKREDYYKILGVDKNASEDEIKKAYRKWALMHHPDQHSGASA-XXXXXXXKLMGVGEAFTILSD>PRK

Parental  KTRYDSGQDLDEEGMNMGDFDANNIFKAFFGGPGGFSFEASGPGNFFFQFG
          KTRY.SGQDLDEEG..MGD.DANNIFKAFF..P.GFSFEASGPGNFFFQFG
Retrocopy KTRYGSGQDLDEEGLYMGDSDANNIFKAFFSSPAGFSFEASGPGNFFFQFG

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	21.57 RPM
SRP051959_heart	0.05 RPM	22.03 RPM
SRP051959_kidney	0.04 RPM	29.57 RPM
SRP051959_liver	0.00 RPM	20.97 RPM
SRP051959_lung	0.07 RPM	27.20 RPM
SRP051959_lymph_node	0.00 RPM	27.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.88 RPM
SRP051959_spleen	0.02 RPM	27.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2475 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475 ,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,