RetrogeneDB ID: retro_mmul_1002

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:103381368..103382248(+)
• 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_1002
GAGATCAAAGACAGTGCATCACAGAAAAGGGATTTCTTAAACAACATATTAATGATTTAAAGGGAACCCTTGCAAAGCTC
CTGGATGAATGATTGGTGACCCTTTTGCAAGAGGTGGGCACCATTAAACAGACCATTAAACCACCACTAGATGATTGCCA
GAAGCTCATAGAACACAGAGTCAACACTCCAGAGGGTTTAGTACGAAAAGGTGAGATTGCCATGGTTGGTGGTGTAGGAG
AAGAGAATGAGAAACTGTGGAGCTTTGCCAAAAAGGCCTTGCATGTTCAGTTGGATGGCATACAAGAAGTTCCTTTACTG
GTTGATGTGCCTTGTTTATCTGCTCAGTTGGATGACTCTATTCTTAACATCATGAAAGACCACATTCTTAAGTATGGAAC
TGTAGCATCTTGCCCACCAGTACAGATAGAAGAACTGATAGAGAAACCTGGAGGCATCATAGTACAATGGTGTAATGTGG
ATGACAACTTTACGGCACAAGATGACAGGCTCCAGTTTTGTAAATGTACTTCAAATCACTTTGAGGATGTATATGTATGT
TCTGAAACTGAATTCATAGTATTGCACATGGACTCCAATGTTGATGATCATTTCAGAATCTGCACCGAGGAGATGGCCGA
CAGGAGCGGAGTCCTTGGAGTGTCTGTCAGATAGTTCATTCCATATTTGTGCCTCATGAGTGGACAGCTGGTTTTGAGGG
GAACAGTCTGAGCAATCAAAGAAATACGTCATGCTGGAACGATTCTGAATATTCAGGTGTTCTCGACTCCAGAGCTCTAA
CTTATTTCTCTGGGCAGACATTAATATTTAGAGTTGAAACTGTGGGACTACAAGACAGAAGAGGCAGTATAGGAGTGTGT

Alignment

ORF - retro_mmul_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIKESASQTRDVL-KQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTAEDLVR
          .IK.SASQ.RD.L.KQH.NDLKGTL.KLLDE.LVTLLQEV.TI.Q....PLDDCQKLIEH.VNT.E.LVR
Retrocopy EIKDSASQKRDFL<KQHINDLKGTLAKLLDE*LVTLLQEVGTIKQTIKPPLDDCQKLIEHRVNTPEGLVR

Parental  EGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRP
          .GEIAM.GGVGEENEKLWSF.KKA.H.QLD...EVPLLVDVPCLSAQLDDSILNI.KDHI.K.GTVAS.P
Retrocopy KGEIAMVGGVGEENEKLWSFAKKALHVQLDGIQEVPLLVDVPCLSAQLDDSILNIMKDHILKYGTVASCP

Parental  PVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCA
          PVQIEELIEKPGGIIV.WC.VDD.FTAQD.RLQF.KCTSNHFEDVYV.SETEFIVLH.D.NVD..FR.C.
Retrocopy PVQIEELIEKPGGIIVQWCNVDDNFTAQDDRLQFCKCTSNHFEDVYVCSETEFIVLHMDSNVDDHFRICT

Parental  -RGDGRQEWSPWSVPQIGHSTLVPHEWTAGFEGYSLSSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFR
          .RGDGRQE.SPWSV.QI.HS..VPHEWTAGFEG.SLS..RN....NDSE.SGVL.SRA.TYF.GQTL.FR
Retrocopy <RGDGRQERSPWSVCQIVHSIFVPHEWTAGFEGNSLSNQRNTSCWNDSEYSGVLDSRALTYFSGQTLIFR

Parental  QLVETVGQPDRRDSIGVC
          ..VETVG..DRR.SIGVC
Retrocopy --VETVGLQDRRGSIGVC

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_1002 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1002 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2133
Pan troglodytes	retro_ptro_1560
Gorilla gorilla	retro_ggor_1649
Pongo abelii	retro_pabe_1925

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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,