RetrogeneDB ID: retro_cjac_1894

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:24871685..24872515(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000015442
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM2
• Ensembl ID: ENSCJAG00000009627
• Aliases: None
• Description: None

Sequence

>retro_cjac_1894
ATGGACACCATCAGTAAGATGCAGATGCTAAAGCTGGGCAAGAAGAACGCCATCCATCTCCCTGAGCAAACCAAAGCCAA
CAAGAAGCAAGCTGAGGACCACTGCAAGCAGCTGGAGGAGGAGCAGAGGAAGCTGAAGGGGACAGAAGATGAAGTAGAAG
AATATTCTGAATCCATGAAGGAGGCCCAGGAGAAACTGCAGTGGGCCGAGCTGGCCAACGATGTTGAGGTGCATGTGGCC
TCCCTAAACCATTGCTTTCAACAGGTAGAGGAGGAGCCAGCCGGGGCCCAGGAGCGCCTGGCCACAGCCCTGAGCAAGCT
AGAAGAGACTGAGAAGGCAGCCAATGAAAAGCCAGAGAGGAATAAAGGTCATAAAAACCTGGCACTTAAGGACAAGAAGA
TGGGGGCGGAGGGGGGAGATTCAGCGAAAGGAGGCCACGTGCATCGCTGAGGATTCAGACCAGAGATACAAGGAGGTGGC
CAGGAAGCTGCTGATCCTGGAGGCAGACCTGGAACACTCAGAAGAGAACTCTGAGGGGGCCAAGAACCGAGTCAGACAGC
TGGAAGAGAAACTTCAAACCATGGACCAGACCCTCAAGTCTCTGATGGCCTCAAGAAGGAGTATTCCACAAAAGAAAATA
AATACGAAGAAATAAATCTGCTGGAGGAGAAGTTGAAGGAAGCTGAGACCAGAGCAGAGTTTGTCAAAAAGTCTATGGCG
AAGTTGGAGAAGACCACCGATGACCTGGAAGAGATGTTGGCCAGTGCCAAGGAGGAGAACGTGGAGATACAGCAGACCTT
GCACCAGACCGTTGGGAACCCAACAACCTA

Alignment

ORF - retro_cjac_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQALQKKLKGTEDEVEKYSESVKEAQEK
          MD.I.K.MQMLKL.K.NAI...EQ..A.KKQAED.CKQLEEE....Q.KLKGTEDEVE.YSES.KEAQEK
Retrocopy MDTISK-MQMLKLGKKNAIHLPEQTKANKKQAEDHCKQLEEE----QRKLKGTEDEVEEYSESMKEAQEK

Parental  LEQAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADE-SERGMKVIENRAMKDEE
          L..AE..A.D.E..VASLN...Q.VEEE...AQERLATAL.KLEE.EKAA.E.S.RG.KVI.........
Retrocopy LQWAEL-ANDVEVHVASLNHCFQQVEEEPAGAQERLATALSKLEETEKAANE>SQRGIKVIKTWHLRTRR

Parental  KMELQEMQLKEAKHIAEDSDRKYEEVARKLVILEGELERSEERAEVAESRARQLEEELRTMDQALKSLMA
          .....E.Q.KEA..IAEDSD..Y.EVARKL.ILE..LE.SEE..E.A..R.RQLEE.L.TMDQ.LKSLMA
Retrocopy WGRRGEIQRKEATCIAEDSDQRYKEVARKLLILEADLEHSEENSEGAKNRVRQLEEKLQTMDQTLKSLMA

Parental  S-EEEYSTKEDKYEEEIKLLEEKLKEAETRAEFAERSVAKLEKTIDDLEETLASAKEENVEIHQTLDQTL
          S...EYSTKE.KY.EEI.LLEEKLKEAETRAEF...S.AKLEKT.DDLEE.LASAKEENVEI.QTL.QT.
Retrocopy S<KKEYSTKENKY-EEINLLEEKLKEAETRAEFVKKSMAKLEKTTDDLEEMLASAKEENVEIQQTLHQTV

Parental  -LELNNL
          ..E.NNL
Retrocopy <WEPNNL

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	0.00 RPM	127.36 RPM
SRP051959_heart	0.00 RPM	200.22 RPM
SRP051959_kidney	0.00 RPM	16.93 RPM
SRP051959_liver	0.00 RPM	17.05 RPM
SRP051959_lung	0.00 RPM	40.93 RPM
SRP051959_lymph_node	0.00 RPM	5.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	471.31 RPM
SRP051959_spleen	0.00 RPM	15.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1894 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1894 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894 ,
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Erinaceus europaeus	ENSEEUG00000005022	1 retrocopy	retro_eeur_31,
Mustela putorius furo	ENSMPUG00000005359	1 retrocopy	retro_mputfur_647,
Otolemur garnettii	ENSOGAG00000011793	1 retrocopy	retro_ogar_988,
Rattus norvegicus	ENSRNOG00000016731	1 retrocopy	retro_rnor_1520,