RetrogeneDB ID: retro_mmul_1280

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:8240170..8240930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4229
• Ensembl ID: ENSMMUG00000013499
• Aliases: None
• Description: None

Sequence

>retro_mmul_1280
GCTCCCCATATCATCGTGGGTACCCCTGGCCAAGTGTTTGATATGCTTAACCGGAGATACCTGTCTCCCAAATACATCAA
GATGTTTGTACTGGACAAAGCTGATGAAATGTTAAGCCGTGGATTCAAGGACCAGATCTATGACATATTCCAAAAGCTTC
ACAGCAACACCCAGGTAGTTTTGCCGTCAGCTACAATGCCTTCTGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGAC
CCCATTCGGATTCTTGTCAAGAAGGAAGAGTTGACCCTGGAGGGTATCCGCCAATTCTACATCAACGTAGAACGAGAAGA
GGGGAAGCTGGACACACTGCGTGATTTGTATGAAACCCTGACCATCACCCAGGCAGTCATCTTCCTCAACACCCAAAGGA
AGGTGGACTGGCTCACCGAGAAGATGCATGCTCGAGATTTCACTGTCTCGGCCATGCATGGAGATACGGACTGAAAAGAA
CGAGACATGATCATGAGGGTGTTTGGTTCTGGCTCTAGCAGAGTTTTGATTACCACTGACCTGCTGGCCAGAGGCAGTGA
TGTGCAGCAGGTTTCTTTAGTCATCAACTACGACCTTCCCACCAATAGGGAAAACATTTCCACAGAACGAGCCGAGGTGG
ACAGTTTGGCCGTAAAGGTGTGGCTATTAACATGGTGACAGAAGAAGACAAGAGGACTCTTCGAGACATCGAGACCTTCT
ACAACACCTCCATGAGGAAATGCGCCTCAATGTTGCTGAC

Alignment

ORF - retro_mmul_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.02 %
• Parental protein coverage: 62.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV
          APHIIVGTPG.VFDMLNRRYLSPKYIKMFVLD.ADEMLSRGFKDQIYDIFQKL.SNTQVVL.SATMPSDV
Retrocopy APHIIVGTPGQVFDMLNRRYLSPKYIKMFVLDKADEMLSRGFKDQIYDIFQKLHSNTQVVLPSATMPSDV

Parental  LEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTE
          LEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREE.KLDTL.DLYETLTITQAVIF.NT.RKVDWLTE
Retrocopy LEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEGKLDTLRDLYETLTITQAVIFLNTQRKVDWLTE

Parental  KMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNREN-YIHR
          KMHARDFTVSAMHGD.D.KERD.IMR.F.SGSSRVLITTDLLARG.DVQQVSLVINYDLPTNREN...HR
Retrocopy KMHARDFTVSAMHGDTD*KERDMIMRVFGSGSSRVLITTDLLARGSDVQQVSLVINYDLPTNREN<HFHR

Parental  IGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSI-EEMPLNVAD
          ..RGG.FGRKGVAINMVTEEDKRTLRDIETFYNTS..EEM.LNVAD
Retrocopy TSRGGQFGRKGVAINMVTEEDKRTLRDIETFYNTSM<EEMRLNVAD

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	49.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	97.89 RPM
SRP007412_cerebellum	0.00 RPM	39.52 RPM
SRP007412_heart	0.00 RPM	41.99 RPM
SRP007412_kidney	0.00 RPM	62.91 RPM
SRP007412_liver	0.00 RPM	105.06 RPM
SRP007412_testis	0.45 RPM	75.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1280 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1280 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_920

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Macaca mulatta	ENSMMUG00000009590	1 retrocopy	retro_mmul_851,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280 ,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,