RetrogeneDB ID: retro_mmul_2119

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:171920503..171920928(-)
• Located in intron of: ENSMMUG00000005148

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSMMUG00000022570
• Aliases: None
• Description: nuclear transcription factor Y subunit beta [Source:RefSeq peptide;Acc:NP_001244649]

Sequence

>retro_mmul_2119
ATGACCTAGGATAGGGGCAGTGCTAGGACACAGGCTTCTCGACTCCGGATTTCTGCAGGCTGCGCTGGAGGAAGTCGTGC
TGCCCAGCCTTGCGTTGACACTGGGAACAGTGTGAATAATCATGAAACCACAGAGGCTTCAAAAGAAAGTTTTGGAGAAT
AAGATATTTGCATTCCCATTGCAGATGCGGCAAGGATCATGAAGAATGTCCCTCAGAGGGCCAGACGGCACAGGACGCCA
AAGAATGTGTTCCAGAGTGTGTGGGTTCATCACCCTCATGGCACGTGAAGCAAGTGAGCGATGCCAGGGAGAGTGAGGAG
ACAGTCAGTGGGGAGGGTGCTCTCTCTGCCCTGTCCACCTGAGGCTTTGAGAGTTATGCAGAAGCGCTGGGGGGGTGCCT
TCAGGCACTCAGAGAGGCTAGGAGA

Alignment

ORF - retro_mmul_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.34 %
• Parental protein coverage: 70.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKN
          MT.D..S..T.AS.L.ISA...GGS....QP..DT..S.N.HE.T..SKESF.E.DI..PIA..ARIMKN
Retrocopy MT*DRGSARTQASRLRISAGCAGGSR-AAQPCVDTGNSVNNHETTEASKESFGE*DICIPIADAARIMKN

Parental  AIPQ-TGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQ
          ..PQ..G..A.DAKECV.ECV....S......S.....E...T..GE..L.A.ST.GF.SY.E.L...LQ
Retrocopy -VPQ<EGQTAQDAKECVPECVGSSPSWHVKQVSDA--RESEETVSGEGALSALST*GFESYAEALGGCLQ

Parental  KFREAMK
          ..REA..
Retrocopy ALREARR

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	0.34 RPM	22.52 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	11.66 RPM
SRP007412_cerebellum	0.26 RPM	14.92 RPM
SRP007412_heart	0.00 RPM	6.71 RPM
SRP007412_kidney	1.29 RPM	12.68 RPM
SRP007412_liver	1.07 RPM	7.36 RPM
SRP007412_testis	0.00 RPM	7.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2119 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2119 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2803

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119 , retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,