RetrogeneDB ID: retro_cjac_1839

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:127393564..127394416(+)
• Located in intron of: ENSCJAG00000019548

Retrocopy information

• Ensembl ID: ENSCJAG00000019553
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1839
ATGGATGCCATCAAGAAGATGATGCAGATGCTGAAGCTGGACAAGGAGAACGCCATCGATCGCGCCGAGCAGGCCGAAGC
TGACAAGAAGCAAGCTGAGGATCGCTGCAAGCAGCTGGAGGAGGAGCAGCAGGCCCTCCAGAAGAAGCTGAAGGGGACAG
AGGATGAAGTGAAAAAGTATTCTGAATCCGTGAAGGAGGCCCAGGAGAAACTGGAGCAGGCTGAGAAGAAGGCCACTGAT
GCTGAGGCAGATGTGGCCTCCCTGAACCGCCACATTCAGCTGGTAGAGGAGGAGCTGGACCAGGCCCAGGAGTGCCTGGC
TACAGCCCTGCAGAAGCTGGAGGAGGCTGAGAAGGCAGCTGATGAGAGCAAGAGAGGAATGAAGGTCATCGAAAACCAGG
CCATGAAGGACGAGGAGGAGATGGAGCTGCAGGAGATGCAGCTGAAAGAGGCCAAGCACATCACTGAGGATTCAGACTAC
AAATACGAGGAGGTGGCCAGGAAGCTGGTGATCCTGGAAGGAGAGCTGGAGCGCTCAGAAGAGAGAGTTGAGGTGGCTGA
GAGCCAAACCAGACAGCTGGAGGAGGAACTTCGAACCATGAACCAGGCCCTCAAGTCCTTGATGGCCTCAGAGGAGGAGT
ATTCCACCAAAGAAGATAAAATGAAGAGGAGATCAAACTAGTGGAGGAGAAGCTGAAAGAGGCTAAGACCCGAGCAGAGT
TTGCTGAAAGGTCTGTGGGCAAAGTTGGAGAAAACCATCGATGACCTAGAAGAGATCTTGGCCAATGCCAAGGAGGAGAA
TGTCGAGATTCACCAGACCTTGGACCAGACCCTGCTGGAACTCAACAACCTG

Alignment

ORF - retro_cjac_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQALQKKLKGTEDEVEKYSESVKEAQEK
          MDAIKK.MQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQALQKKLKGTEDEV.KYSESVKEAQEK
Retrocopy MDAIKKMMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQALQKKLKGTEDEVKKYSESVKEAQEK

Parental  LEQAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRAMKDEEK
          LEQAEKKATDAEADVASLNR.IQLVEEELD.AQE.LATALQKLEEAEKAADES.RGMKVIEN.AMKDEE.
Retrocopy LEQAEKKATDAEADVASLNRHIQLVEEELDQAQECLATALQKLEEAEKAADESKRGMKVIENQAMKDEEE

Parental  MELQEMQLKEAKHIAEDSDRKYEEVARKLVILEGELERSEERAEVAESRARQLEEELRTMDQALKSLMAS
          MELQEMQLKEAKHI.EDSD.KYEEVARKLVILEGELERSEER.EVAES..RQLEEELRTM.QALKSLMAS
Retrocopy MELQEMQLKEAKHITEDSDYKYEEVARKLVILEGELERSEERVEVAESQTRQLEEELRTMNQALKSLMAS

Parental  EEEYSTKEDKY-EEEIKLLEEKLKEAETRAEFAERSV-AKLEKTIDDLEETLASAKEENVEIHQTLDQTL
          EEEYSTKEDK..EEEIKL.EEKLKEA.TRAEFAERSV.AKLEKTIDDLEE.LA.AKEENVEIHQTLDQTL
Retrocopy EEEYSTKEDKM<EEEIKLVEEKLKEAKTRAEFAERSV>AKLEKTIDDLEEILANAKEENVEIHQTLDQTL

Parental  LELNNL
          LELNNL
Retrocopy LELNNL

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	0.35 RPM	127.36 RPM
SRP051959_heart	0.26 RPM	200.22 RPM
SRP051959_kidney	0.27 RPM	16.93 RPM
SRP051959_liver	0.19 RPM	17.05 RPM
SRP051959_lung	0.29 RPM	40.93 RPM
SRP051959_lymph_node	0.59 RPM	5.02 RPM
SRP051959_skeletal_muscle	0.48 RPM	471.31 RPM
SRP051959_spleen	0.13 RPM	15.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1839 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1839 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,