RetrogeneDB ID: retro_mmul_998

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:84556826..84557506(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSMMUG00000009069
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:RefSeq peptide;Acc:NP_001244548]

Sequence

>retro_mmul_998
AGTCTCTTGCAAGAGCTGGGCACCATTAAACAGGAGACTATTAAGCCTCTAGGTGACTGCCAGGAGTCATACAGCATGAA
ATTAACACTGCAGAGGACTTAGTCCAAGAAAGTGAGATCACCATTGTTGGTGGCATGGGAGAACAGACTGAGAAACTGTG
AGCCTTTACCAAAAAGGCCTCCTGCATTTAGTTAGACAGGTTACCAGAAGTGTCTCTGCTGGTTGATGTGCCTTGTTTAT
TTGCTCAGTTGAATGACTCAATTCTTATTTTAGTGAAAGCCTACATTTTTCACCATGGAATGGTGCCATCTCACCTACCA
GTAGAAATGTAAGCACTAATAGAGAAAACTGGAAGCCTCATTGTATGATGATGTAAGATAGATGATGACACTATAGCTCA
AGATTACAGATTCCAGCTCCATAAATGTACTTCAAATCATTTTAAGTATGTATGTGTAGGCTCTGAACCTGAATTTATAG
CATTGCACATAGATCCCAATGTTGACTATTAGTTCAGAATCTATGCCAGAGGGCAAAAGACCGGCTGACAGGAGTGGAGT
CCTTGGAGCATCCGCCAGATAGGTTATTCCATTTTGATGCCTCCTGAGTGGACAGCTGGCTTTAAGGGGTATACTCTGAG
CAACTGAAGAAATATATCACTCCAGCTTGATTCTGAATCC

Alignment

ORF - retro_mmul_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLLQEVDTIEQETIKPLDDCQK-LIEHGVNTAEDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLP
          .LLQE..TI.QETIKPL.DCQ...I.H..NTAEDLV.E.EI...GG.GE..EKL..FTKKAS.I.LD.LP
Retrocopy SLLQELGTIKQETIKPLGDCQE<VIQHEINTAEDLVQESEITIVGGMGEQTEKL*AFTKKASCI*LDRLP

Parental  EVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQ
          EV.LLVDVPCL.AQL.DSIL..VK..IF.HG.V.S..PV....LIEK.G..IV..CK.DDD..AQDYR.Q
Retrocopy EVSLLVDVPCLFAQLNDSILILVKAYIFHHGMVPSHLPVEM*ALIEKTGSLIV**CKIDDDTIAQDYRFQ

Parental  FRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGD--GRQEWSPWSVPQIGHSTLVPHEWTAGFE
          ..KCTSNHF..V.VGSE.EFI.LHIDPNVDY.FR..ARG...G.QEWSPWS..QIG.S.L.P.EWTAGF.
Retrocopy LHKCTSNHFKYVCVGSEPEFIALHIDPNVDY*FRIYARGQKTG*QEWSPWSIRQIGYSILMPPEWTAGFK

Parental  GYSLSSRRNIALRNDSES
          GY.LS..RNI.L..DSES
Retrocopy GYTLSN*RNISLQLDSES

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	0.00 RPM	33.05 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.72 RPM
SRP007412_cerebellum	0.00 RPM	20.34 RPM
SRP007412_heart	0.00 RPM	5.89 RPM
SRP007412_kidney	0.00 RPM	5.52 RPM
SRP007412_liver	0.00 RPM	3.64 RPM
SRP007412_testis	0.00 RPM	9.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_998 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_998 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2121
Gorilla gorilla	retro_ggor_1644
Pongo abelii	retro_pabe_1984

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Echinops telfairi	ENSETEG00000017897	1 retrocopy	retro_etel_313,
Felis catus	ENSFCAG00000025986	1 retrocopy	retro_fcat_1916,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998 ,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,
Ictidomys tridecemlineatus	ENSSTOG00000012342	1 retrocopy	retro_itri_1384,