RetrogeneDB ID: retro_cjac_3121

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:28684893..28685639(-)
• Located in intron of: ENSCJAG00000008024

Retrocopy information

• Ensembl ID: ENSCJAG00000032296
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009747
• Aliases: None
• Description: None

Sequence

>retro_cjac_3121
ATGGCTGGAATCACCACCACTGAGGCGGTGAAGTGTAAGATCCAGGTTCTGCAGCAGCAGCAGGCAGATGATGCAGAAGA
GAGAGCTAAGCATCTCCAGCAAGAAGCTGAGGAAAAAAGATGGGCCTGGACCAGGCTGAGGCTGAGGTGGCCTCCTTGAA
CTATAGGACCCAGCAAGTTGAAGAGGAGCTAAATCACACTCAGTAGTGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAG
CAGAAAAAGCTGCTGATGAGAGAGAAAGAGGTATGAAGGTTATTGGAAACCAGGCCTTAAAAGATAAAGAAAAGATGGAA
CTCCTGGAAATCCAACTCAAAGAAGCTAAGCACACTGCAGAAGAGGCAGATAGGAAGTATGAAGAAGGGGTTCGTGAGTT
GGTGATCACTGAAGGAGACCTGGAATGCACAGAGGAACTAGCAGAGCTGGCAGAGTCCCGTTGCCAAAAAATAGATGAGC
AGATCAGACTGACGGACCAGAATCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTTCCCAAAAGAAGAGAAATATGAG
AAAGAGATCAAGATTCTTACTGATAAACTCAAGGAAATGAAGACCTGTGCTGAGTTTACTGAGAGATAGGTAGCCATGCT
GGAAAAGACAATTGATGACTTGGAAGACAAACTGAAATGCACCAAAGAGGAGAACCTCTGTACACAAAGGATGCTGGACC
AGACTCTGCTTGACTTGAATGAAGTG

Alignment

ORF - retro_cjac_3121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQ-ADDAEERAERLQREVE-GERRAREQAEAEVASLNRRIQLVEEELDRAQE
          MAGITT.EAVK.KIQVLQQQ.ADDAEERA..LQ.E.E.G......QAEAEVASLN.R.Q.VEEEL...Q.
Retrocopy MAGITTTEAVKCKIQVLQQQQADDAEERAKHLQQEAE<GKKMGLDQAEAEVASLNYRTQQVEEELNHTQ*

Parental  RLATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEG
          .LATALQKLEEAEKAADE.ERGMKVI.N.ALKD.EKMEL.EIQLKEAKH.AEEADRKYEE..R.LVI.EG
Retrocopy CLATALQKLEEAEKAADERERGMKVIGNQALKDKEKMELLEIQLKEAKHTAEEADRKYEEGVRELVITEG

Parental  DLERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAER
          DLE.TEE.AELAESRC...DEQIRL.DQNLKCLSAAEEKY..KE.KYE.EIKILTDKLKE..T.AEF.ER
Retrocopy DLECTEELAELAESRCQKIDEQIRLTDQNLKCLSAAEEKYFPKEEKYEKEIKILTDKLKEMKTCAEFTER

Parental  SVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          .VA.LEKTIDDLEDKLKCTKEE.LCTQRMLDQTLLDLNE.
Retrocopy *VAMLEKTIDDLEDKLKCTKEENLCTQRMLDQTLLDLNEV

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	68.16 RPM
SRP051959_heart	0.00 RPM	20.50 RPM
SRP051959_kidney	0.00 RPM	33.86 RPM
SRP051959_liver	0.00 RPM	34.29 RPM
SRP051959_lung	0.00 RPM	91.80 RPM
SRP051959_lymph_node	0.00 RPM	96.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.29 RPM
SRP051959_spleen	0.00 RPM	93.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3121 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 37 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,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,