RetrogeneDB ID: retro_mmul_2313

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:133729518..133730305(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPCA
• Ensembl ID: ENSMMUG00000011073
• Aliases: None
• Description: None

Sequence

>retro_mmul_2313
ATGCCTGAGGAAACCTAGACCCAAGACCAACCCATGGAGGTGGAGGAGGCTGAGATATTCACCTTTCAGGCAGAATTGCC
CAGTTGATGTCATTGATCATCAATACTTTCTACTCGAACAAAGAGATCTTTCTGAGAGAGCTCATTTCAAATTCATCAGA
TGCATTGGACAAAATTCAGTATGAAAGCTTGACGGATCCCAGTAAATTAGACTCTGGGAAAGAGCTGCATATTAACCTTA
TACCAAACAAACAAGATCGAACCCTCCCTATTGTGGATACTGGAATTGGAATGACCAAGGCTGACTTGATCAATAACCTT
GGTATATCACCAAGTCTGGGACCAAAGCATTCATGGAAGCTTTGCAGGCTGGTGCAGGTGTCTCTATGATTGGCCATTTC
AGTGTCGGTTTTTATTCTGCTTATTTGGTTGTTGAGAAAGCAACTGTGATCACCAAACATAATGATGATGAGCAGTATGC
CTGGGAGTCTTCAGCAGGGGGATCATTCACAGTGAGGACAGACACAGGTGAACCTATGGGTCGTGGAACAAAGGTTATCC
TACACCTGAAAGAAGACCAAACTGAGTACTTGGAGGAACGAAGAATAAAGGAGATTGTGAAGAAACATTCTCAGTTTATT
GGATATTTCATTATTCTTTTTGTGGAGAAGGAACGTGATAAAGAAGTCAATGATAATGAGGCTGAAGAAAAGGAAGACAG
AGAAGAAGAAAAAGAAAAAGAAGAGAAAGAGTCTGAAGACAAACCTGAAATTGAAGATGTTGGTTCT

Alignment

ORF - retro_mmul_2313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPEETQTQDQPMEEEEVETFAFQAE-IAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSK
          MPEET.TQDQPME.EE.E.F.FQAE.IAQLMSLIINTFYSNKEIFLRELISNSSDALDKI.YESLTDPSK
Retrocopy MPEET*TQDQPMEVEEAEIFTFQAE<IAQLMSLIINTFYSNKEIFLRELISNSSDALDKIQYESLTDPSK

Parental  LDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGT-IAKSGTKAFMEALQAGADISMIGQFGVGF
          LDSGKELHINLIPNKQDRTL.IVDTGIGMTKADLINNLG..I.KSGTKAFMEALQAGA..SMIG.F.VGF
Retrocopy LDSGKELHINLIPNKQDRTLPIVDTGIGMTKADLINNLGI<ITKSGTKAFMEALQAGAGVSMIGHFSVGF

Parental  YSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVK
          YSAYLV.EK.TVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVK
Retrocopy YSAYLVVEKATVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVK

Parental  KHSQFIGYPITLFVEKERDKEVSDDEAEEKEDKEEEKEKEEKESEDKPEIEDVGS
          KHSQFIGY.I.LFVEKERDKEV.D.EA...................KPEIEDVGS
Retrocopy KHSQFIGYFIILFVEKERDKEVNDNEAXXXXXXXXXXXXXXXXXXXKPEIEDVGS

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	1060.33 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	836.06 RPM
SRP007412_cerebellum	0.32 RPM	849.54 RPM
SRP007412_heart	0.00 RPM	332.82 RPM
SRP007412_kidney	0.00 RPM	477.57 RPM
SRP007412_liver	0.04 RPM	426.36 RPM
SRP007412_testis	0.23 RPM	1122.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2313 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2313 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313 ,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,