RetrogeneDB ID: retro_mmul_1024

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:42945651..42946203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSMMUG00000005209
• Aliases: None
• Description: cysteine and histidine-rich domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001244685]

Sequence

>retro_mmul_1024
GATGAAATTAAGATTGGGATTTCATGTAAGAATGGAGGGTGTTCAAAGATATATCGGGGTCTAGAGAGTCTAGAAGAAGT
CTGTGTGTATCATTCTGGAGTACCTATTTTCCACGAGGGAATGAAATACTGGAGCTGTTGTAGAAGAAAAACTTCTGATT
TTAATACATTCTTAGCCCAAGAGGGCTGTACAACAGGGAAACATATGTGGGCTAAAAAGGATGCTGGGGAAAATGTTGTT
CCATGTAGACATGACTGGCATCAGACTGAAGGTGAAGTTACCATTTCAGTATATGCTAAAAATTCACTTCCAGAACTTAG
TCAAGTAGAAGTACATAGCACGTTGTTAAATGTGCACATTGGATTTGAAGGAGAGAAGGAATTTCATCAAAATGTGAAAT
TACGGGATGTGACTGATGTAAAGCGAATTTATGTAACTATGACTGCAACAAAGATTGAGATCACTATAAGAAAAGCTGAA
CCTATGCAGTGGGCAAGCCTTGAACTGCCTGCAGTCAAAAAGCAGCAAAAACAAAAAGACAACACAACAGAT

Alignment

ORF - retro_mmul_1024 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEIKIGTSCKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGCTKGRHMW
          DEIKIG.SCKNGGCSK.YRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGCT.G.HMW
Retrocopy DEIKIGISCKNGGCSKIYRGLESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQEGCTTGKHMW

Parental  TKKDA----VSCQHDWHQTGGEVTISVYAKNSLPELSRVEANSTLLNVHIVFEGEKEFDQNVKLWGVIDV
          .KKDA....V.C.HDWHQT.GEVTISVYAKNSLPELS.VE..STLLNVHI.FEGEKEF.QNVKL..V.DV
Retrocopy AKKDAGENVVPCRHDWHQTEGEVTISVYAKNSLPELSQVEVHSTLLNVHIGFEGEKEFHQNVKLRDVTDV

Parental  KRSYVTMTATKIEINMRKAEPMQWASLELPAAKKQEKQKDDTTD
          KR.YVTMTATKIEI..RKAEPMQWASLELPA.KKQ.KQKD.TTD
Retrocopy KRIYVTMTATKIEITIRKAEPMQWASLELPAVKKQQKQKDNTTD

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	22.19 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	24.83 RPM
SRP007412_cerebellum	0.13 RPM	16.27 RPM
SRP007412_heart	0.06 RPM	15.43 RPM
SRP007412_kidney	0.00 RPM	12.32 RPM
SRP007412_liver	0.00 RPM	4.16 RPM
SRP007412_testis	0.19 RPM	37.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1024 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1024 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2252
Pan troglodytes	retro_ptro_1595
Gorilla gorilla	retro_ggor_1679
Pongo abelii	retro_pabe_1959

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024 , retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,