RetrogeneDB ID: retro_mmus_40

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:24333067..24333514(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000057036
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rpl27a
• Ensembl ID: ENSMUSG00000046364
• Aliases: Rpl27a, L27', L27A, L29
• Description: ribosomal protein L27A [Source:MGI Symbol;Acc:MGI:1347076]

Sequence

>retro_mmus_40
ATGCCATCCAGACTGAGGAAGACCCGGAAACTCCGGGGCCACGTGAGCCACGGCCACGGCCGCATCGGTAAGCACCGCAA
GCACCCAGGCGGCCGCGGGAATGCTGGAGGCATGCACCACCACAGGATCAACTTTGACAAATATCACCCAGGTTACTTTG
GGAAAGTTGGTATGCGGCATTACCACTTGAAGAGGAACCAGAGCTTCTGCCCAACAGTCAACCTGGATAAACTGTGGACA
TTGGTCAGCGAGCAGACACGGGTCAATGCGGCAAAAAACAAGACTGGAGTTGCTCCCATCATTGATGTTGTTCGATCAGG
CTACTACAAAGTTCTGGGCAAGGGAAAGCTCCCTAAGCAACCTGTCATCGTGAAGGCCAAATTCTTCAGCAGAAGAGCTG
AGGAGAAGATTAAGGGTGTTGGAGGTGCCTGTGTTCTGGTGGCTTAA

Alignment

ORF - retro_mmus_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC
          MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC
Retrocopy MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC

Parental  PTVNLDKLWTLVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
          PTVNLDKLWTLVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
Retrocopy PTVNLDKLWTLVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV

Parental  GGACVLVA
          GGACVLVA
Retrocopy GGACVLVA

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	0.09 RPM	49.46 RPM
SRP007412_cerebellum	0.00 RPM	41.68 RPM
SRP007412_heart	0.06 RPM	35.55 RPM
SRP007412_kidney	0.10 RPM	40.66 RPM
SRP007412_liver	0.03 RPM	38.75 RPM
SRP007412_testis	0.05 RPM	21.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_40 was not detected

EST

No EST(s) were mapped for retro_mmus_40 retrocopy.

TSS

No TSS is located nearby retro_mmus_40 retrocopy 5' end.

Lab

retro_mmus_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_40 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 155 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Equus caballus	ENSECAG00000022469	1 retrocopy	retro_ecab_289,
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162, retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Homo sapiens	ENSG00000166441	7 retrocopies	retro_hsap_1263, retro_hsap_1908, retro_hsap_2352, retro_hsap_239, retro_hsap_3335, retro_hsap_3586, retro_hsap_3682,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Microcebus murinus	ENSMICG00000002296	4 retrocopies	retro_mmur_1309, retro_mmur_459, retro_mmur_612, retro_mmur_835,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268,
Monodelphis domestica	ENSMODG00000007480	1 retrocopy	retro_mdom_575,
Mustela putorius furo	ENSMPUG00000012532	3 retrocopies	retro_mputfur_118, retro_mputfur_1362, retro_mputfur_464,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40 ,
Nomascus leucogenys	ENSNLEG00000017535	1 retrocopy	retro_nleu_102,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Ochotona princeps	ENSOPRG00000004717	11 retrocopies	retro_opri_1080, retro_opri_1214, retro_opri_131, retro_opri_203, retro_opri_255, retro_opri_304, retro_opri_570, retro_opri_769, retro_opri_798, retro_opri_836, retro_opri_990,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33,
Pteropus vampyrus	ENSPVAG00000002887	14 retrocopies	retro_pvam_1087, retro_pvam_1130, retro_pvam_1135, retro_pvam_119, retro_pvam_1305, retro_pvam_198, retro_pvam_392, retro_pvam_54, retro_pvam_546, retro_pvam_575, retro_pvam_837, retro_pvam_84, retro_pvam_93, retro_pvam_993,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677, retro_sscr_769, retro_sscr_809,
Tupaia belangeri	ENSTBEG00000000046	20 retrocopies	retro_tbel_1093, retro_tbel_1101, retro_tbel_1148, retro_tbel_1152, retro_tbel_1223, retro_tbel_1338, retro_tbel_1639, retro_tbel_2017, retro_tbel_2606, retro_tbel_2777, retro_tbel_298, retro_tbel_3111, retro_tbel_3496, retro_tbel_3881, retro_tbel_4566, retro_tbel_460, retro_tbel_544, retro_tbel_643, retro_tbel_925, retro_tbel_937,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,
Vicugna pacos	ENSVPAG00000011227	7 retrocopies	retro_vpac_200, retro_vpac_272, retro_vpac_286, retro_vpac_426, retro_vpac_508, retro_vpac_581, retro_vpac_99,