RetrogeneDB ID: retro_mmul_2305

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:100403207..100403633(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000020071
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.17409
• Ensembl ID: ENSMMUG00000003578
• Aliases: None
• Description: 40S ribosomal protein S23 [Source:RefSeq peptide;Acc:NP_001180509]

Sequence

>retro_mmul_2305
ATGGGCAAGTGTCGTGGACTTCGTACTGCTAGGAGGCTCTGTAGTCACTGATGAGATCAGAAGTGGCATGATACAGTACA
AGAAAGCCCATCTGGGCACAGCCCTGAAGGCCAACCCTTTTGGAGGTACTTTTCATGCAAAAGGAATTGTGCTGGAAAAA
GTAGGAGTTGAAGCCAAAAAGCCAAATTCTGCCATTAGGAAGTGTGTCAGGGTCCAGTGGATCAAGGATGGCAAGAAAAT
CACAGCCTTTGTACTCAATGATGATTGCTTGAACTTTACTGAGGAAAACGATAAAGTTGTGGTTGCTGGATTTGGTCAAA
AAGTCATGCTGTTGGTTATATTTCTGGAGTCCGCTTTTGGGTTGTCAAAGTAGCCTATGTCTTTCTTTTGGCCCTATACA
AAGGCAAGAAGGAAAGACCAAGATCA

Alignment

ORF - retro_mmul_2305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPF-GGASHAKGIVLEKVGVEAKQPNSAIRKC
          MGKCRGLRTAR.L.SH..DQKWHD........G......PF.GG..HAKGIVLEKVGVEAK.PNSAIRKC
Retrocopy MGKCRGLRTARRLCSH**DQKWHD-TVQESPSGHSPEGQPF>GGTFHAKGIVLEKVGVEAKKPNSAIRKC

Parental  VRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGR-KGHAVGDIPGVRFKVVKVANVSLLALYKGKK
          VRVQ.IK.GKKITAFV.ND.CLNF.EEND.V.VAGFG..K.HAVG.I.GVRF.VVKVA.V.LLALYKGKK
Retrocopy VRVQWIKDGKKITAFVLNDDCLNFTEENDKVVVAGFGQ<KSHAVGYISGVRFWVVKVAYVFLLALYKGKK

Parental  ERPRS
          ERPRS
Retrocopy ERPRS

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	0.11 RPM	28.46 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	87.82 RPM
SRP007412_cerebellum	0.00 RPM	44.81 RPM
SRP007412_heart	0.00 RPM	78.26 RPM
SRP007412_kidney	0.12 RPM	62.67 RPM
SRP007412_liver	0.00 RPM	74.97 RPM
SRP007412_testis	0.00 RPM	22.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2305 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2305 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 153 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011136	1 retrocopy	retro_acar_85,
Ailuropoda melanoleuca	ENSAMEG00000015966	3 retrocopies	retro_amel_1096, retro_amel_341, retro_amel_751,
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Canis familiaris	ENSCAFG00000030896	7 retrocopies	retro_cfam_1145, retro_cfam_1305, retro_cfam_1415, retro_cfam_1743, retro_cfam_2105, retro_cfam_375, retro_cfam_436,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Cavia porcellus	ENSCPOG00000022705	2 retrocopies	retro_cpor_1182, retro_cpor_1377,
Dipodomys ordii	ENSDORG00000001813	2 retrocopies	retro_dord_187, retro_dord_93,
Equus caballus	ENSECAG00000020523	2 retrocopies	retro_ecab_275, retro_ecab_500,
Erinaceus europaeus	ENSEEUG00000001849	7 retrocopies	retro_eeur_102, retro_eeur_262, retro_eeur_326, retro_eeur_462, retro_eeur_515, retro_eeur_53, retro_eeur_662,
Felis catus	ENSFCAG00000008839	7 retrocopies	retro_fcat_1557, retro_fcat_1601, retro_fcat_1876, retro_fcat_2000, retro_fcat_5, retro_fcat_609, retro_fcat_644,
Homo sapiens	ENSG00000186468	6 retrocopies	retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287, retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla	ENSGGOG00000025014	6 retrocopies	retro_ggor_1316, retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Loxodonta africana	ENSLAFG00000031506	3 retrocopies	retro_lafr_1117, retro_lafr_1216, retro_lafr_606,
Macropus eugenii	ENSMEUG00000012931	1 retrocopy	retro_meug_811,
Microcebus murinus	ENSMICG00000013964	2 retrocopies	retro_mmur_1354, retro_mmur_872,
Myotis lucifugus	ENSMLUG00000013939	2 retrocopies	retro_mluc_1676, retro_mluc_2183,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305 , retro_mmul_852,
Monodelphis domestica	ENSMODG00000020255	3 retrocopies	retro_mdom_1518, retro_mdom_1612, retro_mdom_395,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Mus musculus	ENSMUSG00000049517	12 retrocopies	retro_mmus_2151, retro_mmus_2200, retro_mmus_2690, retro_mmus_2812, retro_mmus_3118, retro_mmus_3163, retro_mmus_3168, retro_mmus_323, retro_mmus_3619, retro_mmus_365, retro_mmus_836, retro_mmus_848,
Nomascus leucogenys	ENSNLEG00000013203	3 retrocopies	retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Otolemur garnettii	ENSOGAG00000008163	11 retrocopies	retro_ogar_1177, retro_ogar_1303, retro_ogar_1785, retro_ogar_1849, retro_ogar_238, retro_ogar_2479, retro_ogar_253, retro_ogar_2695, retro_ogar_2823, retro_ogar_3519, retro_ogar_364,
Pongo abelii	ENSPPYG00000015608	7 retrocopies	retro_pabe_1538, retro_pabe_1585, retro_pabe_19, retro_pabe_2515, retro_pabe_2567, retro_pabe_2716, retro_pabe_3129,
Pan troglodytes	ENSPTRG00000017052	6 retrocopies	retro_ptro_1190, retro_ptro_2056, retro_ptro_2223, retro_ptro_2707, retro_ptro_3075, retro_ptro_3122,
Pteropus vampyrus	ENSPVAG00000002083	4 retrocopies	retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sorex araneus	ENSSARG00000008904	8 retrocopies	retro_sara_194, retro_sara_346, retro_sara_422, retro_sara_481, retro_sara_540, retro_sara_647, retro_sara_648, retro_sara_714,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92,
Ictidomys tridecemlineatus	ENSSTOG00000000824	3 retrocopies	retro_itri_1418, retro_itri_204, retro_itri_377,
Tarsius syrichta	ENSTSYG00000011385	5 retrocopies	retro_tsyr_1656, retro_tsyr_1946, retro_tsyr_406, retro_tsyr_462, retro_tsyr_933,
Tursiops truncatus	ENSTTRG00000014491	6 retrocopies	retro_ttru_1253, retro_ttru_1555, retro_ttru_186, retro_ttru_458, retro_ttru_487, retro_ttru_578,
Vicugna pacos	ENSVPAG00000009427	7 retrocopies	retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56, retro_vpac_598, retro_vpac_81,