RetrogeneDB ID: retro_cjac_1853

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:146609490..146610530(+)
• Located in intron of: ENSCJAG00000015351

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSCJAG00000000252
• Aliases: None
• Description: None

Sequence

>retro_cjac_1853
GCTGAAAAACTCATGAGCGTTCTGGGAAACTATCGCCACCTTGGTGAAGTGCACACCCACATCCATATGGGCATTGTGGG
CCTTCTCACTATTTGGAAGAGCAGCCTGATTAATAGCCTGAAGCGCAGCCACGCATGCAACGTGGGAGCCATTCCTAGGG
TCATGAAATTCACACAGGAGATCTATCTGGACAAGTTCATTTGGCTGCTGGATGCTCCAGGCATTGTCCCAGGACCCAGC
TCAGAGGTGGGCACCATCCTGCATAACTGCATCCATGTGCAGAGGCTGGCAGACCCCATGACGCCTGTGGAGACCAACCT
ACAGTGCTGCAACCTGGAGTAGATTTCCAACTATTACCGCCTCTCTGGGTTCCAGACCACTGAGCACTTTCTTACAACAG
TCACCCACCATTTGGGAGAGAAGAGAGGCTTATACAGTCAGGAGCAGGAAGCCAAAGCTGTCCTAGCTGACTGCGTGAGC
AAGATCAGCTTCTATAGACCACCACCACCCACTCACATTCTTCCCGCCCATCTCAGCACCGAGATCATTAAGGAAATGAC
CGAGGTCTTTGACATTGAGGATACCAAGCAGGCCAATGAAGACAACATGGAATGCTTGGCCACTGGAGAATGTGATGAGC
TGTTGAATGACACAGACCCATTGGAAATGGAGATCAAGTCTCTCCATTCTCTCATGATGAAAATAGCAGATGCCATTGAA
AATAAAACCACTGTATATAAGATTAGAGATTTCACTGGGTATTGTACCAATCCAAATCGTCATCAGATGATGTGGGCCAA
ACTCAATGTAGACCACCATACTAAAAACAACTGTAGAGTGATGTCTGCCCAATGGACTGCTGCCCAGTACTGCAGAGAAT
CATGGAGATGGACCCTCTGCAACAGAGCTAGGCTCTGGCATCCTCCCTGAAGTATAAGAAGAAGATGCAGATACATGCAG
ATAAAATCACCAGGGAGCTGTCTGATTCCCTGATGTCTGCCCTTGACCTCTCTGGCAATGGTGATGATCATGTTGGTGAC

Alignment

ORF - retro_cjac_1853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 60.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AENLMRILGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACSVGAVPGITKFMQEVHLDKFIRLL
          AE.LM..LGNY..LGEV.THI..G.VGL....KSSLINSLKRS.AC.VGA.P...KF.QE..LDKFI.LL
Retrocopy AEKLMSVLGNYRHLGEVHTHIHMGIVGLLTIWKSSLINSLKRSHACNVGAIPRVMKFTQEIYLDKFIWLL

Parental  DAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGISGFQTTEHFLTAVAHRLGK
          DAPGIVPGP.SEVGTIL.NC.HVQ.LADP.TPVET.LQ.CNLE.ISNYY..SGFQTTEHFLT.V.H.LG.
Retrocopy DAPGIVPGPSSEVGTILHNCIHVQRLADPMTPVETNLQCCNLE*ISNYYRLSGFQTTEHFLTTVTHHLGE

Parental  KKKGGLYSQEQAAKAVLADWVSGKISFYISPPPTHTLPAHLSAEIVKEMTEVFDIEDTEQANEDTMECLA
          K...GLYSQEQ.AKAVLAD.VS.KISFY..PPPTH.LPAHLS.EI.KEMTEVFDIEDT.QANED.MECLA
Retrocopy KR--GLYSQEQEAKAVLADCVS-KISFYRPPPPTHILPAHLSTEIIKEMTEVFDIEDTKQANEDNMECLA

Parental  TGESDELLGDTDPREMEIKLLHSPMMKIADAIENKTTVYKIGDLTGYCTNPNRHQMGWAKRNVNHHPKNN
          TGE.DELL.DTDP.EMEIK.LHS.MMKIADAIENKTTVYKI.D.TGYCTNPNRHQM.WAK.NV.HH.KNN
Retrocopy TGECDELLNDTDPLEMEIKSLHSLMMKIADAIENKTTVYKIRDFTGYCTNPNRHQMMWAKLNVDHHTKNN

Parental  NMV-DVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSMMSALDLSASGDDSVG
          ..V.DVC..D..PVLQRIME.DPLQQ..ALAS.LK.KKKMQ..ADKI...LSDS.MSALDLS..GDD.VG
Retrocopy CRV<DVCPMDCCPVLQRIMEMDPLQQS*ALASSLKYKKKMQIHADKITRELSDSLMSALDLSGNGDDHVG

Parental  D
          D
Retrocopy D

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	0.75 RPM	17.02 RPM
SRP051959_heart	0.61 RPM	23.05 RPM
SRP051959_kidney	0.53 RPM	25.96 RPM
SRP051959_liver	0.35 RPM	19.10 RPM
SRP051959_lung	0.47 RPM	23.13 RPM
SRP051959_lymph_node	0.80 RPM	28.86 RPM
SRP051959_skeletal_muscle	0.50 RPM	34.18 RPM
SRP051959_spleen	0.48 RPM	32.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1853 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1853 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3327
Gorilla gorilla	retro_ggor_1296
Pongo abelii	retro_pabe_2742
Macaca mulatta	retro_mmul_2084

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591, retro_cjac_1853 ,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742,