RetrogeneDB ID: retro_mmul_2534

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:126377435..126378089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG3
• Ensembl ID: ENSMMUG00000002116
• Aliases: None
• Description: protein BTG3 [Source:RefSeq peptide;Acc:NP_001252970]

Sequence

>retro_mmul_2534
CAGACAATTGAGAGGTTTGCTGAGAAATTGACTCTAATATTTCAAGAAAAATATAAATAATTTTTTTGTCCTGAAATCTC
TCAGAAGTACAGATCTACATATGTATGCCTGTCAATAAGTGTCAAAAAGTTGATCCAGGTATCCTGAAGGCCCATCAGAA
CAGCTTTATCTTGTATAGCAATCTGTGATTGCCTAAGGTGCTAACTTTCTAGGTGGACCTATGAGAGGTGTGCTGTCAGT
ATGGAGAAAAATAACAATGCACTAATTGTTGCCAGCTTTGAAAATGTAGTTCAGAACAAGCATCAGATCTGAAAGAAAAG
TTCTAGGGCCTTTCGACATGGCTACCTCTGATTATCATTAAGCATCCTCTTCTTCACATGAAAAAAATGTAAGGAAGTAA
AACCCAATTTTGGTGAATGCAACCCCTAGTTCTGCATATCAGATTTTTGAATTGATATTCTTTCCTTTTCCAATATGGTG
TTCTTTTGTCCAGAAAAAAAAATGAATGTACCAAGAAAATGGTCATCAGACTCACTACCCTACTCTTGCTCCGTTAGTTA
TCCACATTAGGGAAGGAAAAATAAATTGCATATTAAAATTGCAGCGACATGGGTACCTCCTCCTGTAATTCACTGTGACT
AAAATCACTGGATT

Alignment

ORF - retro_mmul_2534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.02 %
• Parental protein coverage: 87.3 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EAVERFAEKLTLILQEKYKNHWYPE-KPSKGQAYRCIRVNKFQRVDPDVLKACENSCILYSDLGLPKELT
          ...ERFAEKLTLI.Q........PE...S..Q.Y.C..VNK.Q.VDP..LKA..NS.ILYS.L.LPK.LT
Retrocopy QTIERFAEKLTLIFQXXXXXXXXPE<NLSEVQIYICMPVNKCQKVDPGILKAHQNSFILYSNL*LPKVLT

Parental  LWVDPCEVCCRYGEK-NNAFIVASFENEDENKDEISRKVTRA-LDKVTSDYHSGSSSSDEETSKEMEVKP
          ..VD..EVCC.YGEK.NNA.IVASFEN...NK..I..K..RA..D..TSDYH..SSSS.E.........P
Retrocopy F*VDL*EVCCQYGEK>NNALIVASFENVVQNKHQI*KKSSRA>FDMATSDYH*ASSSSHEKNVR--K*NP

Parental  NSVTAAASPVYQISELIFPPLPMWHPLPRKKPGMYRGNGHQNHYPPPVPF-GYPNQGRKNKPYRPIPVTW
          ..V.A..S..YQI.ELIF.P.P.W.........MY..NGHQ.HYP...P...YP..GRKNK....I..TW
Retrocopy ILVNATPSSAYQIFELIFFPFPIWCSFVQXXX*MYQENGHQTHYPTLAPL<SYPH*GRKNKLHIKIAATW

Parental  VPPPGMHCDRNHWI
          VPPP..HCD.NHWI
Retrocopy VPPPVIHCD*NHWI

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	6.05 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.44 RPM
SRP007412_cerebellum	0.00 RPM	0.90 RPM
SRP007412_heart	0.00 RPM	5.54 RPM
SRP007412_kidney	0.00 RPM	6.22 RPM
SRP007412_liver	0.00 RPM	0.99 RPM
SRP007412_testis	0.00 RPM	19.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2534 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2534 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_4118

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003406	1 retrocopy	retro_cjac_4118,
Dasypus novemcinctus	ENSDNOG00000012987	2 retrocopies	retro_dnov_1703, retro_dnov_2682,
Macaca mulatta	ENSMMUG00000002116	1 retrocopy	retro_mmul_2534 ,
Mustela putorius furo	ENSMPUG00000010746	1 retrocopy	retro_mputfur_849,
Mus musculus	ENSMUSG00000022863	1 retrocopy	retro_mmus_225,
Otolemur garnettii	ENSOGAG00000013303	8 retrocopies	retro_ogar_1693, retro_ogar_1755, retro_ogar_2575, retro_ogar_2769, retro_ogar_2795, retro_ogar_3346, retro_ogar_524, retro_ogar_551,
Ochotona princeps	ENSOPRG00000012837	1 retrocopy	retro_opri_381,
Ictidomys tridecemlineatus	ENSSTOG00000010285	1 retrocopy	retro_itri_617,
Tarsius syrichta	ENSTSYG00000006151	5 retrocopies	retro_tsyr_1172, retro_tsyr_1406, retro_tsyr_1753, retro_tsyr_231, retro_tsyr_495,