RetrogeneDB ID: retro_cjac_2362

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:105920760..105921984(+)
• Located in intron of: ENSCJAG00000006246

Retrocopy information

• Ensembl ID: ENSCJAG00000006301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MKRN2
• Ensembl ID: ENSCJAG00000016733
• Aliases: None
• Description: makorin ring finger protein 2 [Source:HGNC Symbol;Acc:7113]

Sequence

>retro_cjac_2362
AGGTACTTTATGCATGGTGTGTGTCGGGAAGGAAGCCAGTGCTTATTCTCACATGACTTGGCAAGCAGCAAGCCGTCCAC
CATCTGCAAGTACTACCAGAAAGGCTACTGTGCCTATGGAACTCGGTGCAGATATGACCACACAAGGCCCTCTGCTGCAG
CTGGAGGTGCTGTGGGCACCATGGCCCACAATGTACCCTCTCCGACTTTTCACAGTCCTCACCCTCCTTCTGAGGTCACT
GCATCCATTGTGAAAACTAACTCACATGAACCTGGGAATCGTGAAAAGAGAACATTGGTTCTCAGAGACCGAAATCTCTC
TGGCATGGCTGAAGGAAAGACTAACCCGAGCATGGTGAGTAATCTAGGCAGCTGCAGTGACTCCCAGCCCAGCCCCGAGA
TGAAGCCGACTTCCTACCTAGATGCCATTAGGAGTGGCCTTGATGACCTGGAGGCCAGCAGCTCCTACAACAATAAGCAG
CAGCTGTGCCCCTATGCAGCTGCTGGGGAGTGCCGATTTGGGGATGCCTGTGTCTACCTGCACAGGGAGGTCTGTGAAAT
CTGTAGGCTGCGAGTCTTGCACCCCTTCGACCCAGAGCAGAGGAAGGCTCACGAAAAGATCTGCATGTTGACATTCGAAC
ATGAGATGGAGAAGGCCTTTGCCTTCCAAGCAAGCCAGGACAAAGTGTGCAGTATCTGCATGGAAGTGATCCTGGAGAAG
GCCTCTGCTTCTGAGAGGAGATTTGGGATTCTCTCCAATTGCAATCACACGTACTGCTTGTCCTGCATCCGACAGTGGCG
GTGTGCCAAACAATTTGAAAACCAAATCATTAAGTCTTGTCCAGAATGCTGTGTGATATCAGAGTTTGTAATTCCAAGTG
TGTATTGGGTGGAAGATCAGAATAAAAAGAACGAGTTGATTGAAGCTTTCAAACAGGGGATGGGGAAAAAAGCCTGTAAA
TACTTTGAGCAAGGCAAGGGGACCTGCCCATTTGGAAGCAAATGCCTTTATCGACATGCTTACCCTGATGGGCAGCTAGC
AGAGCCTGAGAAACCTCAGAAACAGCTCAGTTCTCAAGGCACTGTGAGGTTCTTTAATTCAGTGCGGCTCTGGGATTTCA
TTGAGAACCGAGAAAGCCAGCATGTCCCCAACAATGAAGATGTCGACATGACAGAGCTTGGGGACCTCTTCATGCACCTT
TCTGGAGTGGAGTCATCAGAACCC

Alignment

ORF - retro_cjac_2362 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.28 %
• Parental protein coverage: 98.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYFMHGVCREGSQCLFSHDLANSKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF
          RYFMHGVCREGSQCLFSHDLA.SKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF
Retrocopy RYFMHGVCREGSQCLFSHDLASSKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF

Parental  HSPHPPSEVTASIVKTNSHEPGKREKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL
          HSPHPPSEVTASIVKTNSHEPG.REKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL
Retrocopy HSPHPPSEVTASIVKTNSHEPGNREKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL

Parental  DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLHGEVCEICRLRVLHPFDPEQRKAHEKICML
          DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLH.EVCEICRLRVLHPFDPEQRKAHEKICML
Retrocopy DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLHREVCEICRLRVLHPFDPEQRKAHEKICML

Parental  TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC
          TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC
Retrocopy TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC

Parental  PECRVISEFVIPSVYW-EDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDGRLAEPE
          PEC.VISEFVIPSVYW.EDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDG.LAEPE
Retrocopy PECCVISEFVIPSVYWVEDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDGQLAEPE

Parental  KPRKQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP
          KP.KQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP
Retrocopy KPQKQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP

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	6.94 RPM
SRP051959_heart	2.07 RPM	17.17 RPM
SRP051959_kidney	1.29 RPM	8.52 RPM
SRP051959_liver	0.58 RPM	6.82 RPM
SRP051959_lung	1.20 RPM	9.65 RPM
SRP051959_lymph_node	0.91 RPM	10.02 RPM
SRP051959_skeletal_muscle	2.42 RPM	23.63 RPM
SRP051959_spleen	1.28 RPM	10.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2362 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2362 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Callithrix jacchus	ENSCJAG00000016733	1 retrocopy	retro_cjac_2362 ,
Mus musculus	ENSMUSG00000000439	2 retrocopies	retro_mmus_3578, retro_mmus_544,
Otolemur garnettii	ENSOGAG00000003255	1 retrocopy	retro_ogar_3196,
Pteropus vampyrus	ENSPVAG00000005822	1 retrocopy	retro_pvam_1177,