RetrogeneDB ID: retro_cjac_4128

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:129035955..129036908(+)
• Located in intron of: None

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_4128
AACCCTTTAACTAAGATGAAGCCGATCAACTAGGTGAATGAGCGAGAGGTCAAGTTTGGGGTGGCCGATAAGGTGTCCTG
GCACTCTGAGTACAAGGACAGCACCTGGATCTTCCTGGGAGGGCTTCCTTATGAACTGACTGAAGGGGACATCATCTGTG
TGTTCTCACAATATGAGGAGATGGTTAACATTAATCTCATGCAGGACAAGAAGACTGGGAAATCCAAACGATTCTGTTTC
CTCTGCTATGAAGACCAAAGGAGCATAATTCTGGCTGTTGACAATTCTAATGGGATCAAGATCAAAGGAAGAACTATCTG
AGTGGATCATGTATCTAACTATCAGGCTCCTAAGGATTCAGAAGAAATGGATGATGTGTCCAAAGAGCTCCAGGAGAAAG
GCTGTGGGGCTCGTACCCCCTCACCAAGTTAGTTTAAGGGCTCTGAAAATGAAAACCCAACAAAAAAGCACAACAAAGAC
AAAAAGGGAAAAAAGAAAGAAAAAGAGAAAACTGACCGGGAGGTACAGGCAGATCAACCATCCTCATTGTCACCCAGAAG
CAAGACAGTAAAGGAAAAAGATGATGACCCTGGCCCTAAGAAGCACAGCAGCAAGAACTCAGAGAGAGCTGAAAAGTCAG
AGCCCAGGGAGGGGCAGAAGCTCCCCAAGGCCAGGACTGCCTACTCCGGTAGAGTAGAGGACCTAGAGAGGAAGCTGAAT
GAGAAACCCAAGCACCAGCACAAGTCCTCAAGCAGGAAGGAGGCAAGAGAAGAAAAGACTCAGGGACAGAGGGCAGAGCT
CAGACACATTCTAGCCAGCACAATGGGCATTCTGAAGGGCATGGTCATAGAAGTAGAAGTAGGATCTGAGTTAAATTCCA
TAGTCATAAAAGGTCCCATTCTCCCGGGAGTGGGAGTCTTTGAATCCCAGTGATAGTACGCATCACTGAAGAC

Alignment

ORF - retro_cjac_4128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 92.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPLTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGEIVNINLVRDK
          .PLTK.K.IN..NEREV..GVADKVSWHSEYKDS.WIFLGGLPYELTEGDIICVFSQY.E.VNINL..DK
Retrocopy NPLTKMKPIN*VNEREVKFGVADKVSWHSEYKDSTWIFLGGLPYELTEGDIICVFSQYEEMVNINLMQDK

Parental  KTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEEMDDVTRELQEKGCGARTP
          KTGKSK.FCFLCYEDQRS.ILAVDN.NGIKIKGRTI.VDHVSNY.APKDSEEMDDV..ELQEKGCGARTP
Retrocopy KTGKSKRFCFLCYEDQRSIILAVDNSNGIKIKGRTI*VDHVSNYQAPKDSEEMDDVSKELQEKGCGARTP

Parental  SPSLSKSSEDEKPTKKHKKDKKEKKKRKKEKEKTDREIQAEQPSSSSPRSKTVKKK-DDPGPKRHSSKNS
          SPS..K.SE.E.PTKKH.KDKK.KKK...EKEKTDRE.QA.QPSS.SPRSKTVK.K.DDPGPK.HSSKNS
Retrocopy SPS*FKGSENENPTKKHNKDKKGKKK---EKEKTDREVQADQPSSLSPRSKTVKEKDDDPGPKKHSSKNS

Parental  ERAQKSEPREGQKLPKARTAYSGGAEELERELKKEKPKHEHKSSSKREAREEKTRDRDRRRAQTHILAST
          ERA.KSEPREGQKLPKARTAYSG..E.LER.L..EKPKH.HKSSS..EAREEKT.....R....HILAST
Retrocopy ERAEKSEPREGQKLPKARTAYSGRVEDLERKL-NEKPKHQHKSSSRKEAREEKT--QGQRAELRHILAST

Parental  TGVPKGIVIEVEVGAEINPIGIKGP-GAPGSGSLPIPVTVGVTED
          .G..KG.VIEVEVG.E.N.I.IKGP...PGSGSL.IPV.V..TED
Retrocopy MGILKGMVIEVEVGSELNSIVIKGP<HSPGSGSL*IPVIVRITED

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	0.02 RPM	2.31 RPM
SRP051959_heart	0.09 RPM	3.56 RPM
SRP051959_kidney	0.20 RPM	3.95 RPM
SRP051959_liver	0.28 RPM	2.75 RPM
SRP051959_lung	0.10 RPM	4.98 RPM
SRP051959_lymph_node	0.02 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.98 RPM
SRP051959_spleen	0.15 RPM	4.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4128 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4128 has 0 orthologous retrocopies within eutheria group .

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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,