RetrogeneDB ID: retro_mmul_2399

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:47868948..47869499(+)
• Located in intron of: ENSMMUG00000013836

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2512
• Ensembl ID: ENSMMUG00000007551
• Aliases: None
• Description: ribosomal protein L13a [Source:RefSeq peptide;Acc:NP_001182348]

Sequence

>retro_mmul_2399
GTGGCGGAGGGGCAGGTCCCGGTGATGGAGGCCGAGGCCACCTCCTGGGCCACCTGGCGGCCGTTGTGGCGAAGCAGGTA
CTGCTGGGCTGGAAGGTGGTGGTGCGCTGCGAGGGCATCAACGTTTCTGACAGTTTCTACAGAAATAAGCTGAAGTAGCC
GGCCTTTTTCCGCAGGCGGATGAACACCAACCCTGACGAGGGGCCCATTATTTCCTGGCCCCCAGCAGCTTCTTCTAGCA
GACAGTGCAGGGCCCGCTGCCCACAAGACCCAGCGAGGCCAGGCTGCCCTGGACCCCGAGGTGTTCGATGGAATCCCACT
GCCCTACAACAGGAAAACCAGATGGGGGTTCCTGCTGCACGCAAGGCTGTGCATTTGAAGCCCACGAGAGAGTTTGCCTA
TGTGGGGCGCCTGGCTCAAGAGGCTGGCTGGAAGTACCAGGCAGTGACAGCTACCCTGGAGGAGAAGAAGAAAGAGAAGG
CCGAGACCCGCTACCAGAAGAAGAAATAGCTCATGAGACTGCAGAAAGAGGCCGAAAAGAACGTGGAGAGG

Alignment

ORF - retro_mmul_2399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 92.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEVQVLVLD-GRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRG
          .AE.QV.V...GRGHLLG.LAA.VAKQVLLG.KVVV.RCEGIN.S..FYRNKLK..AF.R.RMNTNP..G
Retrocopy VAEGQVPVME<GRGHLLGHLAAVVAKQVLLGWKVVV-RCEGINVSDSFYRNKLK*PAFFRRRMNTNPDEG

Parental  P-YHFRAPSRIFWRTVRGMLP-HKTKRGQAALDRLKVFDGIPPPYDKKKR-MVVPAALKVVRLKHTRKFA
          P...F.APS..F..TV.G.LP.HKT.RGQAALD...VFDGIP.PY..K.R.M.VPAA.K.V.LK.TR.FA
Retrocopy P<HYFLAPSSFF*QTVQGPLP<HKTQRGQAALDP-EVFDGIPLPYNRKTR<MGVPAARKAVHLKPTREFA

Parental  YLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEK
          Y.GRLA.E.GWKYQAVTATLEEK.KEKA...Y.KKK.LMRL.K.AEKNVE.
Retrocopy YVGRLAQEAGWKYQAVTATLEEKKKEKAETRYQKKK*LMRLQKEAEKNVER

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	89.42 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	247.11 RPM
SRP007412_cerebellum	0.00 RPM	122.30 RPM
SRP007412_heart	0.00 RPM	287.48 RPM
SRP007412_kidney	0.00 RPM	220.18 RPM
SRP007412_liver	0.00 RPM	266.72 RPM
SRP007412_testis	0.00 RPM	123.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2399 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2399 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_671
Callithrix jacchus	retro_cjac_972

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 142 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Cavia porcellus	ENSCPOG00000012417	2 retrocopies	retro_cpor_1000, retro_cpor_888,
Equus caballus	ENSECAG00000015832	3 retrocopies	retro_ecab_388, retro_ecab_653, retro_ecab_773,
Erinaceus europaeus	ENSEEUG00000014071	6 retrocopies	retro_eeur_168, retro_eeur_310, retro_eeur_315, retro_eeur_484, retro_eeur_562, retro_eeur_618,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Felis catus	ENSFCAG00000009194	4 retrocopies	retro_fcat_1197, retro_fcat_1649, retro_fcat_324, retro_fcat_548,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Microcebus murinus	ENSMICG00000009318	6 retrocopies	retro_mmur_240, retro_mmur_283, retro_mmur_311, retro_mmur_359, retro_mmur_65, retro_mmur_736,
Myotis lucifugus	ENSMLUG00000004945	10 retrocopies	retro_mluc_1015, retro_mluc_1342, retro_mluc_1836, retro_mluc_1894, retro_mluc_2219, retro_mluc_2221, retro_mluc_2427, retro_mluc_2471, retro_mluc_2506, retro_mluc_675,
Macaca mulatta	ENSMMUG00000007551	14 retrocopies	retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399 , retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mustela putorius furo	ENSMPUG00000002604	3 retrocopies	retro_mputfur_1418, retro_mputfur_853, retro_mputfur_935,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Nomascus leucogenys	ENSNLEG00000005211	23 retrocopies	retro_nleu_1173, retro_nleu_1429, retro_nleu_1568, retro_nleu_159, retro_nleu_1823, retro_nleu_1873, retro_nleu_1892, retro_nleu_1897, retro_nleu_2047, retro_nleu_228, retro_nleu_2398, retro_nleu_2415, retro_nleu_2463, retro_nleu_2614, retro_nleu_2789, retro_nleu_2928, retro_nleu_330, retro_nleu_392, retro_nleu_441, retro_nleu_475, retro_nleu_513, retro_nleu_744, retro_nleu_760,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Ochotona princeps	ENSOPRG00000001194	3 retrocopies	retro_opri_316, retro_opri_764, retro_opri_806,
Procavia capensis	ENSPCAG00000004086	4 retrocopies	retro_pcap_163, retro_pcap_290, retro_pcap_415, retro_pcap_416,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pan troglodytes	ENSPTRG00000011298	1 retrocopy	retro_ptro_31,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,
Tarsius syrichta	ENSTSYG00000008791	4 retrocopies	retro_tsyr_1363, retro_tsyr_437, retro_tsyr_620, retro_tsyr_920,
Tursiops truncatus	ENSTTRG00000005485	7 retrocopies	retro_ttru_1304, retro_ttru_1736, retro_ttru_629, retro_ttru_735, retro_ttru_833, retro_ttru_971, retro_ttru_995,