RetrogeneDB ID: retro_cjac_2487

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:150160682..150161461(-)
• Located in intron of: ENSCJAG00000019580

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABPA
• Ensembl ID: ENSCJAG00000013817
• Aliases: None
• Description: None

Sequence

>retro_cjac_2487
ATGACTAAAAGAAAAGCAGAGGAGCTGACAGAAATTGAGATTAATGGAACAGAGAAACAAGAGTACACAGAAGAAGGCAC
TGTAGAACAAACCTACATACCAGCTGAATTGTGTAAGCCAGGTCACAGACATCAATGAACCAATAGGCGACTTAAAGAAA
CTGCTAGAACCAAGACTACAGTGTTCTCTGGATGCTCACGACATTTGCCTGCAAGATGCCTAGCTGGATCCAGAACAAAG
TTTATTTGACCAAGGAATGAAGACAGATGGAACTGTACAGCTTAGTGTATGGGTAATTTCTTACCAAGGAATTGAACCAA
AGTTAAACATCCTTGAAACTGTTAAACCTGTGGACACTGTTGAAGGTGTTACTGATCCAGATGCTCACCATGCTGAATCA
GAAGCACACCTTGTTGAAGAAGCTCAAGTGATAACTCTTGATGGCACAGAACACATCACAAACATTTCAGATGAAACTTC
AGAACAAGTAAAGAAGATGGGCTGCTGCACTGGAAGGCTATAGAAAAGAACAAGAATGCCTTGGGATATCCTATGATCCC
ATACAGTGGTCCACAGACCAAGTCCTGCATTGGATGGCTTGGGTAATGAAGGAATTCAGCATAACTGATATAGACCTCAT
CACACTCAACCTTTCCAGAAGAGAATTATGTAGTCTCAACCAAGATTTTTTTCAGTGGGTTCCTCTGGGAGAAATTCTCT
GGAGTCATCTGTAACTTCTCTGAAAATATGTATTGACAAGAACAACAGATGAATGAAAT

Alignment

ORF - retro_cjac_2487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.1 %
• Parental protein coverage: 57.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTKREAEELIEIEIDGTEKPECTEESIVEQTYAPAE-CVSQAIDINEPIGNLKKLLEPRLQCSLDAHEIC
          MTKR.AEEL.EIEI.GTEK.E.TEE..VEQTY.PAE.CVSQ..DINEPIG.LKKLLEPRLQCSLDAH.IC
Retrocopy MTKRKAEELTEIEINGTEKQEYTEEGTVEQTYIPAE>CVSQVTDINEPIGDLKKLLEPRLQCSLDAHDIC

Parental  LQDIQLDPERSLFDQGVKTDGTVQLSVQVISYQGIEPKLNILEIVKPADTVEVVIDPDAHHAESEAHLVE
          LQD..LDPE.SLFDQG.KTDGTVQLSV.VISYQGIEPKLNILE.VKP.DTVE.V.D..............
Retrocopy LQDA*LDPEQSLFDQGMKTDGTVQLSVWVISYQGIEPKLNILETVKPVDTVEGVTDXXXXXXXXXXXXXX

Parental  EAQVITLDGTKHITTISDETSEQV-TRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMT
          EAQVITLDGT.HIT.ISDETSEQV..RWAAALEGYRKEQE.LGI.YDPIQWSTDQVLHW..WVMKEFS.T
Retrocopy EAQVITLDGTEHITNISDETSEQV>RRWAAALEGYRKEQECLGISYDPIQWSTDQVLHWMAWVMKEFSIT

Parental  DIDLTTLNISGRELCSLNQEDFFQRVPRGEILWSHLELLRKYVLASQEQQMN
          DIDL.TLN.S.RELCSLNQ.DFFQ.VP.GEILWSHL.LL.KYVL.......N
Retrocopy DIDLITLNLSRRELCSLNQ-DFFQWVPLGEILWSHL*LL*KYVLTRTTDE*N

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	0.60 RPM	20.50 RPM
SRP051959_heart	0.61 RPM	32.15 RPM
SRP051959_kidney	1.09 RPM	27.22 RPM
SRP051959_liver	0.54 RPM	33.55 RPM
SRP051959_lung	0.85 RPM	42.39 RPM
SRP051959_lymph_node	1.03 RPM	38.45 RPM
SRP051959_skeletal_muscle	0.09 RPM	28.45 RPM
SRP051959_spleen	1.13 RPM	43.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2487 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002592	1 retrocopy	retro_cjac_1312,
Callithrix jacchus	ENSCJAG00000008102	1 retrocopy	retro_cjac_4220,
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487 ,
Dasypus novemcinctus	ENSDNOG00000016059	1 retrocopy	retro_dnov_476,
Homo sapiens	ENSG00000154727	1 retrocopy	retro_hsap_3737,
Ochotona princeps	ENSOPRG00000009283	1 retrocopy	retro_opri_1174,
Pan troglodytes	ENSPTRG00000013810	1 retrocopy	retro_ptro_2536,
Tursiops truncatus	ENSTTRG00000004785	1 retrocopy	retro_ttru_154,