RetrogeneDB ID: retro_cjac_3040

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:155327135..155328075(-)
• Located in intron of: ENSCJAG00000005653

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX2
• Ensembl ID: ENSCJAG00000002436
• Aliases: None
• Description: RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282]

Sequence

>retro_cjac_3040
AAGGCGAAGCCGATCAACCAACTGAATGAGTGACAGGTCCAGCCTGGGGTGGTCGATAAGGTGTCCTGTGACTCCAAGTG
CAAGGACGGCGCCTGGATCTTCCTGGGAGGGCTTCCTTATGAACTGAATGAAGGGGACATCATCTGTGTGTTCTCACAAC
ATGGCGAGATTGTTAACATTCATCTTGTGCCGGACAAAAGAATGGGAAATCCAAAGGATTCCATTTCCTCTCCTAGGGAG
ACCAGAGGAGCACAATTCTGGCTGTTGACAATTTAAATGGGATTAAGATCAAAGGAAGAACTATCTGAGTGGATCAAGTG
TCTAACCACCGAGTACCTAAGGAGTCAGGAGAAATAGAGGATGTCACCCGAGAGCTCCAGAGAAGGGCTGTGGGGCTCGT
ACTTCCTCACCAAGTTTGTCTCAGAGCTCCGAAAATGACAAACCAACACAAAAGCACAAAAAAGACAAACAGGAAAAAAA
GGAAAGAAAGAAAGAGAGAAAACTGACTGGGAGGTACAGGCAGTGCAACCATCCTCTTCATCATTCGGAAACGAGACAGC
AAAGGAAAAGGATGACCTGGCCCTAAGAAACACAGCAACAAGAACTCAGAGATAGCTCAGAAGCCAGAGCCCAGGGAGGG
GCGGAAGCTCCCCGGGGCCAGGACTGCCTACTCTGGTGGAGCAGAGGACCTAGAGCCGGAGCTGAAGGAGGAGAAATCGA
ACCACAAGCCTAAGTCCTCAAGCAGGAGAGAGGCAAAAGAAAAGACCAGGGATAGGGACAGAGGGCGGAGTCAGACACAC
ATTGTAGCCTGTACAACGGGCGTTCTGAAGGGTGTAGTCATGGGGTTGAAGTAGGAGCTGAGATAAATCTCAGAGGCATA
AAAGGGCCTGGCGCTCCCGGGAGCCTTCGAATCCCAGTGACCATAGGCTTCAGTGAAGAT

Alignment

ORF - retro_cjac_3040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGEIVNINLVRDK-KTG
          K.K.IN.LNE..VQ.GV.DKVS..S..KD.AWIFLGGLPYEL.EGDIICVFSQ.GEIVNI.LV.DK.K.G
Retrocopy KAKPINQLNE*QVQPGVVDKVSCDSKCKDGAWIFLGGLPYELNEGDIICVFSQHGEIVNIHLVPDK<KNG

Parental  KSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEEMDDVTRELQ-EKGCGARTPSP
          KSKGF.FL...DQRSTILAVDN.NGIKIKGRTI.VD.VSN.R.PK.S.E..DVTRELQ.EKGCGART.SP
Retrocopy KSKGFHFLS*GDQRSTILAVDNLNGIKIKGRTI*VDQVSNHRVPKESGEIEDVTRELQ<EKGCGARTSSP

Parental  SLSKSSEDEKPTKKHKKDKKEKKKRKKEKEKTDREIQAEQP-SSSSPRSKTVKKKDD-PGPKRHSSKNSE
          SLS.SSE..KPT.KHKKDK.EKK.RKKE...T.R..Q...P.SSS.....T.K.KDD.PGPK.HS.KNSE
Retrocopy SLSQSSENDKPTQKHKKDKQEKKERKKERKLTGRYRQCNHP<SSSF-GNETAKEKDD<PGPKKHSNKNSE

Parental  RAQKSEPREGQKLPKARTAYSGGAEELERELKKEKPKHEHKSSSKREAREEKTRDRDRRRAQTHILASTT
          .AQK.EPREG.KLP.ARTAYSGGAE.LE.ELK.EK..H..KSSS.REA..EKTRDRDR.R.QTHI.A.TT
Retrocopy IAQKPEPREGRKLPGARTAYSGGAEDLEPELKEEKSNHKPKSSSRREAK-EKTRDRDRGRSQTHIVACTT

Parental  GVPKGIVI-EVEVGAEINPIGIKGPGAPGSGSLPIPVTVGVTED
          GV.KG.V...VEVGAEIN..GIKGPGAP..GSL.IPVT.G..ED
Retrocopy GVLKGVVM<GVEVGAEINLRGIKGPGAP--GSLRIPVTIGFSED

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	0.60 RPM	2.31 RPM
SRP051959_heart	0.30 RPM	3.56 RPM
SRP051959_kidney	0.27 RPM	3.95 RPM
SRP051959_liver	0.22 RPM	2.75 RPM
SRP051959_lung	0.59 RPM	4.98 RPM
SRP051959_lymph_node	0.34 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.35 RPM	4.98 RPM
SRP051959_spleen	0.21 RPM	4.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3040 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3040 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002436	2 retrocopies	retro_cjac_3040 , retro_cjac_4128,
Equus caballus	ENSECAG00000008257	1 retrocopy	retro_ecab_664,
Echinops telfairi	ENSETEG00000001763	1 retrocopy	retro_etel_1004,
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2,