RetrogeneDB ID: retro_cjac_3961

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286435.1:160429..161483(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1
• Ensembl ID: ENSCJAG00000015104
• Aliases: None
• Description: None

Sequence

>retro_cjac_3961
TCTCCTGAATATGAGAGAGAACCAAATCACAATAAATCTTTAGCTGCAGGTGTGTGGGGCCTACACACCCAAACACACAC
ATACCCAACCAAAAAAATCTCCCAAGCTCCTCTCTTAGAATATCCTCCGAATCCTAAATCTAGAGCTCCAAGGATGCTGG
TCATTAAGAAAGGTAATACCAAAGACTGACAGCTGTCTGGATTCCCAGTAGTAGGAAATCTTCAGTCACAGCCAGTTAAG
AATGGAACTGGTCCAAGTGTTTATAAAGGTTTAGTCCCTAAACCTGCTGCTACACCTACAAAACTTACACAATGGAAAAG
CCAAACAAAAGAAAATAAAGTTGGAACTTCTTTCCCTCATAAGTCTACATATGGTATTGGCTACTTTAATGCTTTTAAAT
CAACTGCCAAGAATTTTAGTCCATCAACAAATTCAGTGAAAGAGTTTAATCATTCAAATTCCTCTTCCTCTGTTGATAAA
CTTAATCAGCAGCCTTGTCTAACCAAACTGACATGAATGCATACTGATAAGAAGAGTGAATTTTTGAAAGCAATAAGAGA
CAGAGTAGAAGAGGAACATGAAGATGAAGGCCGTGCTGGCTCAGAGGGATGACGACTCATGTAATTTACATAACAGCAAT
AGTACTCACCAAGAAAGGGATATAAACCAACACTTCAATGAAAATGAAATTTCTCAAGAGAATGGCAATGCCTCAGTGAT
TTCCCAACAGATCATTCAATCTTCAACCTTCCCACAAACTGATGTTCTTTCAAGTTTGCTTGAGGCAGAACACAGATTGT
TAAAGGAAATGGGCTGGCAGGAAGACAGTGAAAATGATGAAACATGTGCTCCCTTAACTAAGGATGAAATGAGAGAATTC
CAAGTTATTAGTGAACAGTTACAGAAGAATGGTCTTAGAAAAAATGGCATTTTGAAAAATGGCCTGATCTGTGACTTCAA
GTTAGGACCCTGGAAGAACAGCATTTTCAAACCCACAGTTGAGAATGATGACACAGAAACAAGTAGCAGTGACACATCAG
ATGACGACAATGTG

Alignment

ORF - retro_cjac_3961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPEYEREPNHNKSLAAGVWGLHAQTHTYPTKKISQAPLLEYPPNPKSRAPRMLVIKKGNTKDLQLSGFPV
          .PEYEREPNHNKSLAAGVWGLH.QTHTYPTKKISQAPLLEYPPNPKSRAPRMLVIKKGNTKD.QLSGFPV
Retrocopy SPEYEREPNHNKSLAAGVWGLHTQTHTYPTKKISQAPLLEYPPNPKSRAPRMLVIKKGNTKD*QLSGFPV

Parental  VGNLQSQPVKNGTGPSVYKGLVPKPAAPPTKPTQWKSQTKENKVGTSFPHESTYGVGNFNAFKSTAKNFS
          VGNLQSQPVKNGTGPSVYKGLVPKPAA.PTK.TQWKSQTKENKVGTSFPH.STYG.G.FNAFKSTAKNFS
Retrocopy VGNLQSQPVKNGTGPSVYKGLVPKPAATPTKLTQWKSQTKENKVGTSFPHKSTYGIGYFNAFKSTAKNFS

Parental  PSTNSVKECNRSNSSSPVDKLNQQPRLTKLTRMRTDKKSEFLKALKRDRVEEEHEDESRAGSE-KDDDSF
          PSTNSVKE.N.SNSSS.VDKLNQQP.LTKLT.M.TDKKSEFLKA..RDRVEEEHEDE.RAGSE..DD.S.
Retrocopy PSTNSVKEFNHSNSSSSVDKLNQQPCLTKLT*MHTDKKSEFLKAI-RDRVEEEHEDEGRAGSE>DDD-SC

Parental  NLHNSNSTHQERDINRNFDENEIPQENGNASVISQQIIRSSTFPQTDVLSSSLEAEHRLLKEMGWQEDSE
          NLHNSNSTHQERDIN..F.ENEI.QENGNASVISQQII.SSTFPQTDVLSS.LEAEHRLLKEMGWQEDSE
Retrocopy NLHNSNSTHQERDINQHFNENEISQENGNASVISQQIIQSSTFPQTDVLSSLLEAEHRLLKEMGWQEDSE

Parental  NDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKNGLICDFKFGPWKNSTFKPTVENDDTETSSSDTSD
          NDETCAPLT.DEMREFQVISEQLQKNGLRKNGILKNGLICDFK.GPWKNS.FKPTVENDDTETSSSDTSD
Retrocopy NDETCAPLTKDEMREFQVISEQLQKNGLRKNGILKNGLICDFKLGPWKNSIFKPTVENDDTETSSSDTSD

Parental  DDDV
          DD.V
Retrocopy DDNV

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	0.02 RPM	61.97 RPM
SRP051959_heart	0.07 RPM	50.52 RPM
SRP051959_kidney	0.09 RPM	68.78 RPM
SRP051959_liver	0.09 RPM	56.30 RPM
SRP051959_lung	0.13 RPM	86.80 RPM
SRP051959_lymph_node	0.18 RPM	112.67 RPM
SRP051959_skeletal_muscle	0.02 RPM	46.78 RPM
SRP051959_spleen	0.04 RPM	88.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3961 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015104	1 retrocopy	retro_cjac_3961 ,
Microcebus murinus	ENSMICG00000014678	1 retrocopy	retro_mmur_1198,
Myotis lucifugus	ENSMLUG00000007462	1 retrocopy	retro_mluc_155,
Monodelphis domestica	ENSMODG00000019540	1 retrocopy	retro_mdom_283,
Otolemur garnettii	ENSOGAG00000013991	1 retrocopy	retro_ogar_1077,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678,