RetrogeneDB ID: retro_cjac_1445

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:9527824..9528498(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLDIP2
• Ensembl ID: ENSCJAG00000012566
• Aliases: None
• Description: polymerase (DNA-directed), delta interacting protein 2 [Source:HGNC Symbol;Acc:23781]

Sequence

>retro_cjac_1445
TGGTCCCGGTCTCTGACTGGAGCCCGGTGGCCGAGGTCGCTCTGCGCGGCGGCTGGAACTGGGGCCTTCTTGCCAGCGGT
GACCACAACAACACGGAGGAACCTCTTGTCCCGAAACTGACCAGAGGGCCAAGTGTTGGAGACAGTTGGTGTGTTTGAGG
TGCCAAAACAGAATGGAAAATATGAGACCGAGCAACTCTTCCTTCATGGCGCTTTTGGCTACTGAGGTGTTGTCCTGTTT
CCCTGGCAGGCCAGACTGTATGACCAGGATGTGGCTTCTGCAGCTCCAGAAAAAACAGAGAACCCTGCTGGCCATGGCTC
TAAGGAGGTAAAAGGCAAAACTCACACTTACTATCAGGTGCTGATTGATGCCCGTGACTGCCCACATGTATCTCAGAGAT
CTCAGACAGAAGCTGTGACCTTCTTGGCTAACCATGATGACAGCTGCGTCCTCTATGCCATCCCAGGCCTGGACTATGTC
AGCCATGAAGACATCCTCCCCTACACCTCCACTGATCAGGTTCCCATCCAACATGAGCTCTTTGAAAGATTTCTTCTGTA
CGACCAGACAAAAGCATCCTGTTCTGTGGCTTGGGAGACATTAAGGGCCTGGCAAGAGAAGAATCAACCTGGCTGGAGCT
CTGCGATGTTCACCGCAAAACAACTGAGAACATG

Alignment

ORF - retro_cjac_1445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 61.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WSRSLTGARWPRPLCAEDGTGAFSPAASTTTRRHLSSRNRPEGKVLETVGVFEVPKQNGKYETGQLFLHS
          WSRSLTGARWPR.LCA..GTGAF.PA..TTTRR.L.SRN.PEG.VLETVGVFEVPKQNGKYET.QLFLH.
Retrocopy WSRSLTGARWPRSLCAAAGTGAFLPAVTTTTRRNLLSRN*PEGQVLETVGVFEVPKQNGKYETEQLFLHG

Parental  IFGYRGVVLFPWQARLYDRDVASAAPEKAENPAGHGSKEVKGKTHTYYQVLIDARDCPHISQRSQTEAVT
          .FGY.GVVLFPWQARLYD.DVASAAPEK.ENPAGHGSKEVKGKTHTYYQVLIDARDCPH.SQRSQTEAVT
Retrocopy AFGY*GVVLFPWQARLYDQDVASAAPEKTENPAGHGSKEVKGKTHTYYQVLIDARDCPHVSQRSQTEAVT

Parental  FLANHDDSRALYAIPGLDYVSHEDILPYTSTDQVPIQHELFERFLLYDQTKAPPFVARETLRAWQEKNHP
          FLANHDDS..LYAIPGLDYVSHEDILPYTSTDQVPIQHELFERFLLYDQTKA...VA.ETLRAWQEKN.P
Retrocopy FLANHDDSCVLYAIPGLDYVSHEDILPYTSTDQVPIQHELFERFLLYDQTKASCSVAWETLRAWQEKNQP

Parental  -WLELSDVHRETTENI
          .WLEL.DVHR.TTEN.
Retrocopy <WLELCDVHRKTTENM

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	11.65 RPM
SRP051959_heart	0.00 RPM	28.89 RPM
SRP051959_kidney	0.02 RPM	26.60 RPM
SRP051959_liver	0.02 RPM	25.99 RPM
SRP051959_lung	0.00 RPM	12.64 RPM
SRP051959_lymph_node	0.00 RPM	10.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.21 RPM
SRP051959_spleen	0.00 RPM	16.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1445 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1445 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1445 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018665	1 retrocopy	retro_cfam_2069,
Callithrix jacchus	ENSCJAG00000012566	1 retrocopy	retro_cjac_1445 ,
Oryctolagus cuniculus	ENSOCUG00000007781	1 retrocopy	retro_ocun_1169,