RetrogeneDB ID: retro_cjac_2249

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:81563154..81564131(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003822
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNASEH2B
• Ensembl ID: ENSCJAG00000008585
• Aliases: None
• Description: ribonuclease H2, subunit B [Source:HGNC Symbol;Acc:25671]

Sequence

>retro_cjac_2249
GTGGACTGCGGGGACGGGGTTGGCGCCCGGCAGCACGTGTTCCTGGTTCCAGAATATTTAAAAGATGCTTCAAAGATGAA
AAGTGGGCTTATGTTTGTAAAACTGGTTAACCCGTGTTCAGGAGAAGGAGCCATTTACTTGTTCAATATGTGTCTACAGC
AGCTGTTTGAAGTAAAACTTTTCAAGGAAAAACACCATTCTTGGTTTATAAATCAATCAGTTCAATCAGGAGGTCTTCTC
CACTTTGCCACACCCATGGACCCTCTATTTCTGCTTCTCCACTACCTCATAAAGGCTGATAAGGAGGGGAAGTTTCAGCC
CCTTGATCAAGTTGTGGTAGATAATGTGTTTCCGAATGGCATCTTGTTGCTGAAACTTCCTGGACTTGAGAAGTTACTTC
ACCATGTGACAGAGGAAAGAGAAATAGACAACAAGAAATATTACAAGTACAGCAAAGAGAAGACATTGAAGTGGCTGGAA
AAAAAGGTTAATCAAACTATGGCAGCATTAAAAACCAACGGTGTAAATGTCAGTACCCGGGTGCAGTCAATTGCATTTTT
CTCTGGTGACCGAGTTTCCACTGACAAGGAAGAGGATTACATTCGTTATACCCATGGTCTGATAACTGATTACATCCCTA
AAGAATTAAGTGATGACTTATCTAAATACTTAAGGCTTCCAGAACCTTCAGCCTCATTGCCAAATCCTCCATCAAAGAAA
ATAAAGTTATCAGATGAACCTGTAGAAGCAAAAGAAGATTACACTAAGTTTAATACTAAAGATTTGAAGACTGAAAAGAA
AAATAGCAAAATGACTGCAGCTCAGAAGGCTTTGGCTAAAGTTGACAAGGGTGGAATGAAAAGTATTGATACCTTTTTTG
GTGTAAAGAATAAAAAAAAAATTGGAAAGATTTGAAACTTTGAAAATAAAATCTAGCCAAAATATTTGCATATTACATAT
TTCAATTTTGTCCTTCC

Alignment

ORF - retro_cjac_2249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDCGDGFGARQHVFLVPEYLKDASKKMKNGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKLFKEKHHSWF
          VDCGDG.GARQHVFLVPEYLKDASK.MK.GLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKLFKEKHHSWF
Retrocopy VDCGDGVGARQHVFLVPEYLKDASK-MKSGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKLFKEKHHSWF

Parental  INQSVQSGGLLHFATPMDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPNCILLLKLPGLEKLLHHVTEE
          INQSVQSGGLLHFATPMDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPN.ILLLKLPGLEKLLHHVTEE
Retrocopy INQSVQSGGLLHFATPMDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPNGILLLKLPGLEKLLHHVTEE

Parental  RGNPEIDNKKYYKYSKEKTLKWLEKKVNQTMAALKTNGVNVSTRVQSTAFFSGDRVSTDKEEDYIRYAHG
          R...EIDNKKYYKYSKEKTLKWLEKKVNQTMAALKTNGVNVSTRVQS.AFFSGDRVSTDKEEDYIRY.HG
Retrocopy R---EIDNKKYYKYSKEKTLKWLEKKVNQTMAALKTNGVNVSTRVQSIAFFSGDRVSTDKEEDYIRYTHG

Parental  LISDYIPKELSDDLSKYLKLPEPSASLPNPPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKKNSKMTAAQK
          LI.DYIPKELSDDLSKYL.LPEPSASLPNPPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKKNSKMTAAQK
Retrocopy LITDYIPKELSDDLSKYLRLPEPSASLPNPPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKKNSKMTAAQK

Parental  ALAKVDKSGMKSIDTFFGVKN-KKKLERFETLKIKSSQNICILHISI-CPS
          ALAKVDK.GMKSIDTFFGVKN.KKKLERFETLKIKSSQNICILHISI.CPS
Retrocopy ALAKVDKGGMKSIDTFFGVKN>KKKLERFETLKIKSSQNICILHISI>CPS

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	0.58 RPM	8.30 RPM
SRP051959_heart	1.03 RPM	11.44 RPM
SRP051959_kidney	0.73 RPM	7.08 RPM
SRP051959_liver	0.39 RPM	6.56 RPM
SRP051959_lung	0.94 RPM	11.58 RPM
SRP051959_lymph_node	0.78 RPM	11.99 RPM
SRP051959_skeletal_muscle	0.50 RPM	6.07 RPM
SRP051959_spleen	0.78 RPM	18.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2249 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2249 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020149	1 retrocopy	retro_btau_407,
Callithrix jacchus	ENSCJAG00000008585	1 retrocopy	retro_cjac_2249 ,
Dasypus novemcinctus	ENSDNOG00000010489	1 retrocopy	retro_dnov_2225,
Mus musculus	ENSMUSG00000021932	1 retrocopy	retro_mmus_1752,