RetrogeneDB ID: retro_cjac_4214

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:108905081..108906101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSCJAG00000011811
• Aliases: None
• Description: None

Sequence

>retro_cjac_4214
GATGCCTTGATTATGGAAGAAACAGGGAAAGTCTTAGAGAAAATAAAGGAAATGAAAAAAGGTATTGCTTTTCCCACCAT
CATTTTGGTAAATAACTGTGTATGCCACTTCTCCCCTTTGAAGAGCGACCAGGATTATATTCTCAAGGAAGGTAAGTTGG
TAAAAATTGACCTTGGGGTCCATGTGAATGGCTTCATCACTAATGTAGCTCATACTTTTGTGGCCAATGTAGCTCAGGAG
ACCCAAGTAATAGGGAGGACAGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACACCTGGTCAAACC
TGGAAACCAGAACACACAAGTGACAGAAGCTCAGAACAAAGCTGCCCACTCATTTAACTGTGCTGCAATAGAAGGTATGC
TGTCAAACCAGTGCAAGCAGCATGTCATCGATGGAGGAAAAAATCATTAACCAGAATCGCACAGACCTGCAGAAGGACCA
TGAAAAAGCTGAATTTGAGGTACATGAACTATATGCTGTGGATGTTCTCTTCAGCTCAGGAGAGGGCAAGACCAAGGATA
CATGACAGAGAACCACTATTTACAAATGAGACCCCTCTAAATAGTACAGACTGAAAATGAAAACTACATGTGCCTTCTTC
AGTGAGATGGAAAGGCATTTTGATGTCAGGTCACTTATTTTAAGAGCATTTTAAGATGAGAAGAAGCCTCAGATTGGGTG
TGGTGAAGCGAGCCAAACATGAACTGCTACAATCATTTAATGTTCTCTGTGAGAAGGAGGGTGAATTTGTTGCCCAGTTT
AAGTTTACAGTTCTGCTCATGCCCATTGACCTTATGCAGTAAACCAGTGTCCCTTCAAGCCTGACCTCTATAAGTCTGAG
ATGGAGGTCAAGGATACAGAGCTAAAGGCCCTCCTCCAGAGTTCTGTAAGTCAAAAAACCCAGAAGAAGAAAAAAAAGAG
GTCTCCAATACTGCAGAGAATGCCACCAGTGAGGAAACAGTAGAAGAAAATGAAGCTGGG

Alignment

ORF - retro_cjac_4214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.55 %
• Parental protein coverage: 86.55 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVA
          DA.IMEETGK...K.KEMKKGIAFPT.I.VNNCVCHFSPLKSDQDYILKEG.LVKIDLGVHV.GFI.NVA
Retrocopy DALIMEETGKVLEKIKEMKKGIAFPTIILVNNCVCHFSPLKSDQDYILKEGKLVKIDLGVHVNGFITNVA

Parental  HTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQ
          HTFV..VAQ.TQV.GR.ADVIKAAHLCAEAAL.LVKPGNQNTQVTEA.NK.AHSFNC..IEGMLS.Q.KQ
Retrocopy HTFVANVAQETQVIGRTADVIKAAHLCAEAALHLVKPGNQNTQVTEAQNKAAHSFNCAAIEGMLSNQCKQ

Parental  HVIDG-EKTIIQNPTDQQKKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKT
          HVIDG.EK.I.QN.TD.Q.KDHEKAEFEVHE.YAVDVL.SSGEGK.KD..QRTTIYK.DPSK.Y.LKMKT
Retrocopy HVIDG>EKIINQNRTDLQ-KDHEKAEFEVHELYAVDVLFSSGEGKTKDT*QRTTIYK*DPSK*YRLKMKT

Parental  SRAFFSEVERRFDAMPFTLRAFEDEKK-ARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMP-NG
          ..AFFSE.ER.FD.....LRAF.DEKK..R.GVV..AKHELLQ.FNVL.EKEGEFVAQFKFTVLLMP...
Retrocopy TCAFFSEMERHFDVRSLILRAF*DEKK>LRLGVVKRAKHELLQSFNVLCEKEGEFVAQFKFTVLLMP<H*

Parental  PMRITSGPFEPDLYKSEMEVQDAELKALLQSSASRKTQKKKKKKA-SKTAENATSGETLEVNEAG
          P......PF.PDLYKSEMEV.D.ELKALLQSS.S.KTQKKKKK...S.TAENATS.ET.E.NEAG
Retrocopy PYAVNQCPFKPDLYKSEMEVKDTELKALLQSSVSQKTQKKKKKRS<SNTAENATSEETVEENEAG

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	22.96 RPM
SRP051959_heart	0.00 RPM	19.68 RPM
SRP051959_kidney	0.00 RPM	21.39 RPM
SRP051959_liver	0.00 RPM	19.82 RPM
SRP051959_lung	0.00 RPM	23.21 RPM
SRP051959_lymph_node	0.00 RPM	23.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	32.32 RPM
SRP051959_spleen	0.00 RPM	20.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4214 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214 , retro_cjac_4215,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,