RetrogeneDB ID: retro_mmus_2629

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:20260562..20260954(-)
• Located in intron of: ENSMUSG00000040003

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl28
• Ensembl ID: ENSMUSG00000030432
• Aliases: Rpl28, D7Wsu21e
• Description: ribosomal protein L28 [Source:MGI Symbol;Acc:MGI:101839]

Sequence

>retro_mmus_2629
AATCTGCAATGGATGAAGGTATAGAGCTGCTCCAGTTTTCTGATCAAGAGGAATATGCAGATGTACAGCACTGAGCCCCA
ACATCTGAAAGCCTGCAACTCCTTTCGATACAAAAGGCCTATTCACCAAATGACTGTGGGAGTGGGCCTGCAACCCACAG
GAGAGGAGTTGTATTGGTTCTGAAGTCTAGATTGGGTCAGAGAAAACCAGTGATTTCTTTCCTGAGCACCATCATCAACA
AGAATGTCCTGGCAACACTCAGCAATATCAGGCACATGGCCTATAAGAACCAGTACCACTCCAATCTAAACTTGATAGCC
ACCTGCAGAGCCAAGGTCACTGCTGTGAAGCCTGTGATAGAAGAGGGAGCAGAGTAGCCCACCAAGAGCTCG

Alignment

ORF - retro_mmus_2629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.3 %
• Parental protein coverage: 97.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV-EPAADGKGVVVVMKRRSGQRK
          .LQWM.V..CSSFLIKRN.Q.YSTEP..LKA.NSFRY...IH..TVGV..PA....GVV.V.K.R.GQRK
Retrocopy NLQWMKV*SCSSFLIKRNMQMYSTEPQHLKACNSFRYKRPIHQMTVGV<GPATHRRGVVLVLKSRLGQRK

Parental  PATSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQKPVVVKRKRTRPTKSS
          P..S...T.INKN..ATLS.IRHM..KN.Y...L...A..RA.......KP.V.......PTKSS
Retrocopy PVISFLSTIINKNVLATLSNIRHMAYKNQYHSNLNLIATCRAK--VTAVKP-VIEEGAE*PTKSS

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	0.47 RPM	32.57 RPM
SRP007412_cerebellum	0.17 RPM	34.13 RPM
SRP007412_heart	0.00 RPM	95.91 RPM
SRP007412_kidney	0.06 RPM	78.85 RPM
SRP007412_liver	0.00 RPM	81.84 RPM
SRP007412_testis	0.00 RPM	58.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2629 was not detected

EST

No EST(s) were mapped for retro_mmus_2629 retrocopy.

TSS

No TSS is located nearby retro_mmus_2629 retrocopy 5' end.

Lab

retro_mmus_2629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015980	1 retrocopy	retro_acar_10,
Ailuropoda melanoleuca	ENSAMEG00000003764	15 retrocopies	retro_amel_1006, retro_amel_1099, retro_amel_1155, retro_amel_1369, retro_amel_1393, retro_amel_1465, retro_amel_1737, retro_amel_231, retro_amel_289, retro_amel_33, retro_amel_474, retro_amel_556, retro_amel_630, retro_amel_822, retro_amel_829,
Bos taurus	ENSBTAG00000023343	5 retrocopies	retro_btau_263, retro_btau_433, retro_btau_434, retro_btau_565, retro_btau_891,
Canis familiaris	ENSCAFG00000002585	8 retrocopies	retro_cfam_1009, retro_cfam_1192, retro_cfam_2145, retro_cfam_350, retro_cfam_462, retro_cfam_533, retro_cfam_581, retro_cfam_879,
Callithrix jacchus	ENSCJAG00000000869	1 retrocopy	retro_cjac_218,
Cavia porcellus	ENSCPOG00000012833	2 retrocopies	retro_cpor_127, retro_cpor_214,
Dipodomys ordii	ENSDORG00000012809	2 retrocopies	retro_dord_242, retro_dord_789,
Equus caballus	ENSECAG00000026938	2 retrocopies	retro_ecab_1020, retro_ecab_721,
Felis catus	ENSFCAG00000005639	15 retrocopies	retro_fcat_1045, retro_fcat_1214, retro_fcat_1397, retro_fcat_1404, retro_fcat_1463, retro_fcat_1629, retro_fcat_1663, retro_fcat_171, retro_fcat_233, retro_fcat_484, retro_fcat_575, retro_fcat_786, retro_fcat_904, retro_fcat_910, retro_fcat_942,
Homo sapiens	ENSG00000108107	4 retrocopies	retro_hsap_1503, retro_hsap_1964, retro_hsap_2879, retro_hsap_3380,
Gorilla gorilla	ENSGGOG00000022653	4 retrocopies	retro_ggor_1154, retro_ggor_1427, retro_ggor_1995, retro_ggor_2288,
Loxodonta africana	ENSLAFG00000022257	2 retrocopies	retro_lafr_325, retro_lafr_548,
Macropus eugenii	ENSMEUG00000015744	1 retrocopy	retro_meug_1497,
Myotis lucifugus	ENSMLUG00000023789	1 retrocopy	retro_mluc_325,
Macaca mulatta	ENSMMUG00000015901	1 retrocopy	retro_mmul_68,
Monodelphis domestica	ENSMODG00000000275	1 retrocopy	retro_mdom_1458,
Mustela putorius furo	ENSMPUG00000007450	10 retrocopies	retro_mputfur_1014, retro_mputfur_1050, retro_mputfur_1426, retro_mputfur_470, retro_mputfur_639, retro_mputfur_763, retro_mputfur_804, retro_mputfur_855, retro_mputfur_909, retro_mputfur_951,
Mus musculus	ENSMUSG00000030432	10 retrocopies	retro_mmus_162, retro_mmus_1679, retro_mmus_1911, retro_mmus_2511, retro_mmus_2526, retro_mmus_2606, retro_mmus_2629 , retro_mmus_3149, retro_mmus_362, retro_mmus_738,
Nomascus leucogenys	ENSNLEG00000010503	4 retrocopies	retro_nleu_1287, retro_nleu_2607, retro_nleu_619, retro_nleu_969,
Otolemur garnettii	ENSOGAG00000025533	4 retrocopies	retro_ogar_2078, retro_ogar_788, retro_ogar_809, retro_ogar_892,
Ochotona princeps	ENSOPRG00000000463	1 retrocopy	retro_opri_686,
Petromyzon marinus	ENSPMAG00000008617	1 retrocopy	retro_pmar_10,
Pongo abelii	ENSPPYG00000010417	4 retrocopies	retro_pabe_1691, retro_pabe_1869, retro_pabe_2383, retro_pabe_2778,
Pan troglodytes	ENSPTRG00000011505	4 retrocopies	retro_ptro_1312, retro_ptro_1947, retro_ptro_2297, retro_ptro_3181,
Pteropus vampyrus	ENSPVAG00000007315	2 retrocopies	retro_pvam_359, retro_pvam_38,
Rattus norvegicus	ENSRNOG00000017127	5 retrocopies	retro_rnor_1588, retro_rnor_2117, retro_rnor_243, retro_rnor_610, retro_rnor_855,
Sorex araneus	ENSSARG00000009741	1 retrocopy	retro_sara_643,
Ictidomys tridecemlineatus	ENSSTOG00000008006	1 retrocopy	retro_itri_656,
Tursiops truncatus	ENSTTRG00000002428	5 retrocopies	retro_ttru_1246, retro_ttru_1464, retro_ttru_1668, retro_ttru_696, retro_ttru_936,