RetrogeneDB ID: retro_cjac_2594

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:11743099..11743791(-)
• Located in intron of: ENSCJAG00000021304

Retrocopy information

• Ensembl ID: ENSCJAG00000021309
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEX11B
• Ensembl ID: ENSCJAG00000002223
• Aliases: None
• Description: peroxisomal biogenesis factor 11 beta [Source:HGNC Symbol;Acc:8853]

Sequence

>retro_cjac_2594
ATGGACACCTGGGTCTGCTTCAGTGCTCAGAGCCAAGCCCGGGAGCGGCTGTGTAGGGCCGCCCAGTATGGTTGCTCTCT
TCTTGGCCATGCGCTGCAGAGGCATGGAGCCAGTCCTGAGTTACAGAAACAGATTAGACAGCTGGAGGGCCACCTGAGCC
TTGGAAGAAAGCTTCTACGCCTGGGTAACTCAGCAGATGCTCTTGAGTCAGCCAAAAGAGCTGTTCACCTGTCAGATGTT
GTCCTGAGATTCTGCATCACTGTTAGTCACCTCAATCAAGCCTTGTACTTCGCCTGCGACAATGTCCTGTGGGCTGGAAA
GTCTGGACTGGCTCCTCGTGTGAATCAGGAGAAGTGGGCCCAGCGTTCATTCCGGTACTATTTGTTTTCCCTCATCATGA
ATTTGAGCCGTGATGCTTATGAGATTCGCCTACTGATGGAACAAGAGTCTTCAGCTTGTAGCCGGCAACTGAAAGGTTCC
AGAGGAGGCGTCTCAGGAGGAATTGAAACTGGGGACTTGGGGGACCAGGGACCCCAGGAGGAGGTCTGCCCCAACTGGCT
CTGAAACTTCAGCTCCAAGTCCTGCTCCTGGCTCGAGTCCTTAGAGGTCATCCCCCACTTCTGCTGGATGTGGTCAGAAA
TGCCTGTGATGTCTTCATTCCACCAGACAAACTAGGCCTCTGGCGTTGTGGG

Alignment

ORF - retro_cjac_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 89.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDAWVRFSAQSQARERLCRAAQYACSLLGHALQRHGASPELQKQIRQLEGHLSLGRKLLRLGNSADALES
          MD.WV.FSAQSQARERLCRAAQY.CSLLGHALQRHGASPELQKQIRQLEGHLSLGRKLLRLGNSADALES
Retrocopy MDTWVCFSAQSQARERLCRAAQYGCSLLGHALQRHGASPELQKQIRQLEGHLSLGRKLLRLGNSADALES

Parental  AKRAVHLSDVVLRFCITVSHLNRALYFACDNVLWAGKSGLAPHVDQEKWAQRSFRYYLFSLIMNLSRDAY
          AKRAVHLSDVVLRFCITVSHLN.ALYFACDNVLWAGKSGLAP.V.QEKWAQRSFRYYLFSLIMNLSRDAY
Retrocopy AKRAVHLSDVVLRFCITVSHLNQALYFACDNVLWAGKSGLAPRVNQEKWAQRSFRYYLFSLIMNLSRDAY

Parental  EIRLLMEQESSACSRRLKGSGGGVPAGIETG-GLGGPGTPGGGLPQLALKLRLQVLLLARVLRGHPPLLL
          EIRLLMEQESSACSR.LKGS.GGV..GIETG.GLGGPGTPGGGLPQLALKL.LQVLLLARVLRGHPPLLL
Retrocopy EIRLLMEQESSACSRQLKGSRGGVSGGIETG<GLGGPGTPGGGLPQLALKLQLQVLLLARVLRGHPPLLL

Parental  DVVRNACDLFIPLDKLGLWRCG
          DVVRNACD.FIP.DKLGLWRCG
Retrocopy DVVRNACDVFIPPDKLGLWRCG

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	0.73 RPM	3.15 RPM
SRP051959_heart	0.00 RPM	2.61 RPM
SRP051959_kidney	0.02 RPM	4.48 RPM
SRP051959_liver	0.00 RPM	1.91 RPM
SRP051959_lung	0.00 RPM	2.94 RPM
SRP051959_lymph_node	0.00 RPM	2.74 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.25 RPM
SRP051959_spleen	0.00 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2594 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002223	1 retrocopy	retro_cjac_2594 ,
Otolemur garnettii	ENSOGAG00000000204	1 retrocopy	retro_ogar_3300,