RetrogeneDB ID: retro_cjac_1397

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:46416683..46417533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPC3
• Ensembl ID: ENSCJAG00000035686
• Aliases: None
• Description: None

Sequence

>retro_cjac_1397
ATGGCAGCTCCCAAGCAGCAACTAATGATATCAAGGGCATGTACGAGCTCCTCCTCACTTTTCCCACCTTGGGACAACTG
AATCCTTCTGGTGAGGCACCTGCCAGCTAAGCTGACCGCTGAGGAGAAAGAGGACTTGCTGAAGTACTTTTGGGTGCAGC
TGGTGCATGTCCTGTCAGATAAGGGGCAACTGAAACATGCAGCTTTTGCCACATTCTCTAATGAAAAAGCAGCTATAAAG
CATTCACAAGACTACATCAGCTGAAACTTTTGGGTCATACTTTAGTCCTTGAATTTGCAAAAAAAGCAAGATTGAGTTCA
CTCCCCATGTCCAACTTCAGGCTCTGAAAAAAAAAATGTCTGATTACCCTATAGAAGACGATAAAGAAAAGAAAGAACTT
GGTTATTCAACAGTAAAAAATTGAATTGCACCAAACTATGGGCTGACTTTTCCTTTAAATTCATGCCTCAAGTTTATGTA
CCCACCACCTTCCAGCACAATCCTAGCAAATGTAGTGAATGCTTTGGCAAGTGTGCCTAAGTTCTCTGTTCAGGTCCTTC
ATCTTATGAATAAAATGAATTTGCCCACACCTTTTGGACCAATTACTGTGCGACTTTTCATGTTTGAAGACTGTATGGCA
TTGCATGCACCTCTCCCACCCACATCTCCTCAGCCACCTGAGGAATCTCCTTTGCCAGATGAGGATGAGGAGTTATCTAG
TGAAGAATCAGAATATGAAAGCAGTGATGATGACGACTGACAGAGAATGAAAAAACTATTGGAGTTAGCAAATCTTCAGC
CCAAAAGACCCCAAACAACAAAGCAGTGCTATATGAGGAAAAAAAGAGAA

Alignment

ORF - retro_cjac_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 54.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPEQPLVISRGCTSSSSVSPPRGDRTLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHTAFA
          MAAP.Q.L.ISR.CTSSSS..PP.....LLVRHLPA.LTAEEKEDLLKYF..Q.V.VLSDKG.LKH.AFA
Retrocopy MAAPKQQLMISRACTSSSSLFPPWDN*ILLVRHLPAKLTAEEKEDLLKYFWVQLVHVLSDKGQLKHAAFA

Parental  TFPNEKAAIK-ALTRLHQLKLLGHTLVVEFA-KEQDRVHSPCPTSVSEKKKRSDDPVEDDKEKKELGYLT
          TF.NEKAAIK.A.TRLHQLKLLGHTLV.EFA.K.......P.......KKK.SD.P.EDDKEKKELGY.T
Retrocopy TFSNEKAAIK<AFTRLHQLKLLGHTLVLEFA<KKSKIEFTPHVQLQALKKKMSDYPIEDDKEKKELGYST

Parental  IENGIAPNHGLTFPLNSCLKYMYPPPSSTILANIVNALASVPKFYVQVLHLMNKMNLPTPFGPITARPPM
          ..N.IAPN.GLTFPLNSCLK.MYPPPSSTILAN.VNALASVPKF.VQVLHLMNKMNLPTPFGPIT.R..M
Retrocopy VKN*IAPNYGLTFPLNSCLKFMYPPPSSTILANVVNALASVPKFSVQVLHLMNKMNLPTPFGPITVRLFM

Parental  YEDYMPLHAPLPPTSPQPPEEPPLPDEDEELSSAESEYESSDDEDRQRMNKLMELANLQPKRPKTIKQRR
          .ED.M.LHAPLPP...............EELSS.ESEYESSDD.D.QRM.KL.ELANLQPKRP.T.KQ..
Retrocopy FEDCMALHAPLPPXXXXXXXXXXXXXXXEELSSEESEYESSDDDD*QRMKKLLELANLQPKRPQTTKQCY

Parental  VRKKRK
          .RKKR.
Retrocopy MRKKRE

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	8.39 RPM
SRP051959_heart	0.00 RPM	18.14 RPM
SRP051959_kidney	0.00 RPM	17.73 RPM
SRP051959_liver	0.00 RPM	20.62 RPM
SRP051959_lung	0.00 RPM	19.16 RPM
SRP051959_lymph_node	0.00 RPM	19.75 RPM
SRP051959_skeletal_muscle	0.00 RPM	39.26 RPM
SRP051959_spleen	0.00 RPM	21.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1397 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1397 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2800
Pan troglodytes	retro_ptro_1897
Pongo abelii	retro_pabe_2224
Macaca mulatta	retro_mmul_1435

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035686	1 retrocopy	retro_cjac_1397 ,
Homo sapiens	ENSG00000185946	1 retrocopy	retro_hsap_2800,
Macaca mulatta	ENSMMUG00000018039	1 retrocopy	retro_mmul_1435,
Nomascus leucogenys	ENSNLEG00000012013	1 retrocopy	retro_nleu_1539,
Nomascus leucogenys	ENSNLEG00000015566	1 retrocopy	retro_nleu_1538,
Pongo abelii	ENSPPYG00000001102	1 retrocopy	retro_pabe_2224,
Pan troglodytes	ENSPTRG00000033902	1 retrocopy	retro_ptro_1897,