RetrogeneDB ID: retro_cjac_1493

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:969582..970244(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013519
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: REXO2
• Ensembl ID: ENSCJAG00000012434
• Aliases: None
• Description: RNA exonuclease 2 [Source:HGNC Symbol;Acc:17851]

Sequence

>retro_cjac_1493
GGAAAGTCATCAGGCAGACTTTAAAGCCAAGGCATTAAGACGATGGAAGTCACTATGTTCATGCCAGGAACATCCTTGGA
ACACAGCACCATTTCCACTGGCACCCAGGTGCCTATACTGGACATTGAGAAGGACCAGATTGTTGAGATAGCCTGTCTGA
TAACTGACTCTGATCTCAACATTTTGGCTGAAGGTCCTAACCTGATTATAAAACAACCAGATGAGTTGCTGGACAGCATG
TCAGATTGGTGTAAGGAGCATCATGGGAAGTCTGGTCATACCAAGGCAGTGAGGGAGAATCCAATTACATTGCAGCTGGC
AGAGTATGAATTTCTATCCTTTTATGACAGCAGACTCCTCTGGGGCTCTGTTCACTTACAGGAAATTCAGTCCATGCAGA
TAAGAAGTATCTTGACAAATACATGCCCCAGTTCATGAAACATCTTCACTGCAGCATAACTGATGCGAGCACCTTTAAAG
AGCTGTCCAGACACTGGTATCCAGAAGAATCTGAATTTGCACCAAAGAAGGCTGCTTCTCACAGGGCTCTTGTGACGTTA
GTGAAAGCATCAAAGAACTTCACTTTTACTAAAATAACGTCTTCAAGGAAAAAAACAGATGAAAAGAAGAGGAAAATTAT
AGAAAATGAGAAGACAGTGAGC

Alignment

ORF - retro_cjac_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.81 %
• Parental protein coverage: 94.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGSRGRFGARGVREGGEAM-AAGESMAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLII
          G.S.GR....G.......M...G.S..............LDIEKDQI.E.ACLITDSDLNILAEGPNLII
Retrocopy GKSSGRL*SQGIKTMEVTMFMPGTSLEHSTISTGTQVPILDIEKDQIVEIACLITDSDLNILAEGPNLII

Parental  KQPDELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSF-VRQQTPPGLCPLAGNSVHADKKFLD
          KQPDELLDSMSDWCKEHHGKSG.TKAV.E..ITLQ.AEYEFLSF...QQTP.GLC.L.GNSVHADKK.LD
Retrocopy KQPDELLDSMSDWCKEHHGKSGHTKAVRENPITLQLAEYEFLSF<L*QQTPLGLCSLTGNSVHADKKYLD

Parental  KYMPQFMKHLHYRIIDVSTVKELCRRWYPEEYEFAPKKAASHRAL-DDISESIRELQFYQNNIFK-KKTD
          KYMPQFMKHLH..I.D.ST.KEL.R.WYPEE.EFAPKKAASHRAL..D.SESI.EL.FY.NN.FK.KKTD
Retrocopy KYMPQFMKHLHCSITDASTFKELSRHWYPEESEFAPKKAASHRAL<CDVSESIKELHFY*NNVFK>KKTD

Parental  EKKRKIIENGENEKTVS
          EKKRKIIEN...EKTVS
Retrocopy EKKRKIIEN---EKTVS

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	0.04 RPM	13.58 RPM
SRP051959_heart	0.02 RPM	10.03 RPM
SRP051959_kidney	0.04 RPM	15.57 RPM
SRP051959_liver	0.06 RPM	13.67 RPM
SRP051959_lung	0.00 RPM	11.47 RPM
SRP051959_lymph_node	0.02 RPM	10.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.62 RPM
SRP051959_spleen	0.00 RPM	9.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1493 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1493 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013497	1 retrocopy	retro_chof_40,
Callithrix jacchus	ENSCJAG00000012434	1 retrocopy	retro_cjac_1493 ,
Dipodomys ordii	ENSDORG00000011255	1 retrocopy	retro_dord_374,
Equus caballus	ENSECAG00000005988	1 retrocopy	retro_ecab_572,
Myotis lucifugus	ENSMLUG00000009030	1 retrocopy	retro_mluc_1861,
Monodelphis domestica	ENSMODG00000013913	1 retrocopy	retro_mdom_1575,
Tarsius syrichta	ENSTSYG00000002237	1 retrocopy	retro_tsyr_1177,