RetrogeneDB ID: retro_mmul_2084

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:58587573..58588611(-)
• Located in intron of: ENSMMUG00000021812

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSMMUG00000008231
• Aliases: None
• Description: None

Sequence

>retro_mmul_2084
TTTGGAGCTGAAAACCTCATGAGGGTTCTGGGGAACTATTGCCACCTTGGTGAAGTGTGCACCCACATCAATATGGGTGT
TGTGGGCCTTCCCAATGTTGGGAAGAGCAGCCTGATTAATAGCCTGAAGCACAGCCATGCATGCCGCGTGGGAGCCGTTC
CTGGGGTCACAAAATTCATGCAGGAGGTCTACCTGGACAAGTTCATCTGGCTGCTGGATGCTCTAGCCATTGTCCCAGGG
CCCAGCTCCGAGGTGGGCACCATTCTGCATAGTTGCATCCACGTGCAGAGGCTGGCAGACGCGGTAACCCCAGTGGAGAC
CATCTTGCAGAGCTGCAACCTGGAGATTTCCAACTATTACCTCCTCTCTGGGTACCAGACCACTGAGCACTTTCTGATGG
CAGTGGCCCATCATTTGGGGAAGAGAGACTTATGCAGTCAGGAGCAGGCAGCCAAAGCTGTCCTAGCTGACTGGGTGAGC
GGGAAGATCAGCTTCTATAACCACCACCACCCACTCACACTGCCTGCCTATCTCAGCACTGAGATCATTAAGGAAATGAC
CAAGGTCTTTCACATTGAGAATACCGAGCAGTCAATGAAGACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAGGT
GTTGGGTGACTTGGACCCACTCAAAATGGAGATCAAGTTGCTCCATTATCCGATGATGAAAATAGCAGATGCCATTGAAA
ATAAAGCCACCATGTATAAGATCGGAGATCTCACTGGGTATTGCACCAATCCAAATCGTCATCAGAAGGGGTGGGGCTAA
ACTCAATGTGGATCACCACCCTAAAAACAACAGTAAAGTGGATGTGTGCCCAGTGGACTGCTGCCCAGTACTGCGGAGGA
TCATGGGGATGGACTCCCTATAACAGGGCCAGGCTCTGGCATCCTCCCTAAAGAATAAGAATATGCAGAAATGTGCAGAT
AAAATCGCCAGGGAGCTGTCTGATTCCATGATGTCTGCCGTCAACCTCTCTGGCAATGTTGATGGCGGTGTTGATGAC

Alignment

ORF - retro_mmul_2084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.4 %
• Parental protein coverage: 60.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FGAENLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACSVGAVPGITKFMQEVYLDKFIR
          FGAENLMRVLGNYC.LGEV.THI..GVVGLPNVGKSSLINSLK.S.AC.VGAVPG.TKFMQEVYLDKFI.
Retrocopy FGAENLMRVLGNYCHLGEVCTHINMGVVGLPNVGKSSLINSLKHSHACRVGAVPGVTKFMQEVYLDKFIW

Parental  LLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGVSGFQTTEHFLTAVAHRL
          LLDA..IVPGP.SEVGTIL..C.HVQ.LAD.VTPVETILQ.CNLE.ISNYY..SG.QTTEHFL.AVAH.L
Retrocopy LLDALAIVPGPSSEVGTILHSCIHVQRLADAVTPVETILQSCNLE-ISNYYLLSGYQTTEHFLMAVAHHL

Parental  GKKKKGGLYSQEQAAKAVLADWVSGKISFYIPPPPTHTLPTHLSAEIVKEMTEVFDIEDTEQA-NEDTME
          GK.....L.SQEQAAKAVLADWVSGKISFY....P..TLP..LS.EI.KEMT.VF.IE.TEQ..NEDTME
Retrocopy GKRD---LCSQEQAAKAVLADWVSGKISFYNHHHPL-TLPAYLSTEIIKEMTKVFHIENTEQS<NEDTME

Parental  CLAAGESDELLGDTDPLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNPNHHQMGW-AKRNVDHC
          CLA.GESDE.LGD.DPL.MEIKLLH.PM.KIADAIENK.T.YKIGDLTGYCTNPN.HQ.GW.AK.NVDH.
Retrocopy CLATGESDEVLGDLDPLKMEIKLLHYPMMKIADAIENKATMYKIGDLTGYCTNPNRHQKGW>AKLNVDHH

Parental  PKSNNMVDVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSMMSALDLSGNADD
          PK.N..VDVC.VD..PVL.RIM..D.L.QGQALAS.LKN.K.MQK.ADKIA..LSDSMMSA..LSGN.D.
Retrocopy PKNNSKVDVCPVDCCPVLRRIMGMDSL*QGQALASSLKN-KNMQKCADKIARELSDSMMSAVNLSGNVDG

Parental  GVGD
          GV.D
Retrocopy GVDD

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
SRP007412_brain	0.11 RPM	5.71 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	6.19 RPM
SRP007412_cerebellum	0.00 RPM	9.49 RPM
SRP007412_heart	0.06 RPM	7.60 RPM
SRP007412_kidney	0.00 RPM	11.50 RPM
SRP007412_liver	0.08 RPM	5.78 RPM
SRP007412_testis	0.04 RPM	2.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2084 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2084 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
Callithrix jacchus	retro_cjac_1853

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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,