RetrogeneDB ID: retro_mmus_3304

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:108331307..108331535(+)
• Located in intron of: ENSMUSG00000007815

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps15a
• Ensembl ID: ENSMUSG00000008683
• Aliases: Rps15a, A630031B11Rik
• Description: ribosomal protein S15A [Source:MGI Symbol;Acc:MGI:2389091]

Sequence

>retro_mmus_3304
GAGAAGAGAGGCAAACTCTAGGTCCTGATCAGGCCATACTTCAGAGTTATTGTTTGGTTCCTAACTGTGATAACAAAACA
TGGTTACATTGGTGAATTAGAGGTCATTGATGATTACAGAGTTGGGGAAATCGATGTGAACCTCAAAGGCAGGTTGAATA
AGTAAGTGCAGAGCCCTAGATTTGATATGTAACTCAGAGACCTAGAAAAATGGCAGAATGGTTACATT

Alignment

ORF - retro_mmus_3304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 59.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFDVQLKDLE
          EKRGK..VLIRP...VIV.FLTV..KHGYIGE.E.IDD.R.G.I.VNL.GRLNK..V.SPRFD..L.DLE
Retrocopy EKRGKL*VLIRPYFRVIVWFLTVITKHGYIGELEVIDDYRVGEIDVNLKGRLNK-*VQSPRFDM*LRDLE

Parental  KWQNNLL
          KWQN...
Retrocopy KWQNGYI

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	0.05 RPM	97.00 RPM
SRP007412_cerebellum	0.22 RPM	80.50 RPM
SRP007412_heart	0.06 RPM	56.78 RPM
SRP007412_kidney	0.06 RPM	53.23 RPM
SRP007412_liver	0.11 RPM	40.94 RPM
SRP007412_testis	0.09 RPM	60.70 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3304 was not detected

EST

No EST(s) were mapped for retro_mmus_3304 retrocopy.

TSS

No TSS is located nearby retro_mmus_3304 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: TGGGTATCAAGTGGTTCAGA (20 nt long)
• Reverse primer: CCAGGATTTCTCCTCACTTA (20 nt long)
• Annealing temperature: 50 °C
• (Expected) product size: 542
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 150 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020733	5 retrocopies	retro_btau_14, retro_btau_171, retro_btau_3, retro_btau_57, retro_btau_98,
Callithrix jacchus	ENSCJAG00000020071	6 retrocopies	retro_cjac_120, retro_cjac_128, retro_cjac_170, retro_cjac_231, retro_cjac_359, retro_cjac_80,
Felis catus	ENSFCAG00000010625	11 retrocopies	retro_fcat_125, retro_fcat_1712, retro_fcat_1745, retro_fcat_1951, retro_fcat_1966, retro_fcat_34, retro_fcat_37, retro_fcat_655, retro_fcat_665, retro_fcat_879, retro_fcat_9,
Gadus morhua	ENSGMOG00000005862	1 retrocopy	retro_gmor_16,
Latimeria chalumnae	ENSLACG00000011476	1 retrocopy	retro_lcha_55,
Loxodonta africana	ENSLAFG00000026996	13 retrocopies	retro_lafr_1161, retro_lafr_1201, retro_lafr_210, retro_lafr_236, retro_lafr_247, retro_lafr_309, retro_lafr_323, retro_lafr_356, retro_lafr_571, retro_lafr_613, retro_lafr_629, retro_lafr_759, retro_lafr_956,
Mustela putorius furo	ENSMPUG00000013424	12 retrocopies	retro_mputfur_1022, retro_mputfur_1124, retro_mputfur_1165, retro_mputfur_1296, retro_mputfur_1404, retro_mputfur_1417, retro_mputfur_1505, retro_mputfur_43, retro_mputfur_448, retro_mputfur_589, retro_mputfur_591, retro_mputfur_772,
Mus musculus	ENSMUSG00000008683	29 retrocopies	retro_mmus_1133, retro_mmus_1337, retro_mmus_1863, retro_mmus_2022, retro_mmus_2086, retro_mmus_2108, retro_mmus_2428, retro_mmus_2461, retro_mmus_2515, retro_mmus_2580, retro_mmus_2608, retro_mmus_2609, retro_mmus_2680, retro_mmus_2779, retro_mmus_2842, retro_mmus_3161, retro_mmus_3293, retro_mmus_3304 , retro_mmus_3348, retro_mmus_3352, retro_mmus_3442, retro_mmus_3482, retro_mmus_357, retro_mmus_408, retro_mmus_670, retro_mmus_757, retro_mmus_768, retro_mmus_816, retro_mmus_928,
Otolemur garnettii	ENSOGAG00000013199	14 retrocopies	retro_ogar_102, retro_ogar_1254, retro_ogar_1302, retro_ogar_1361, retro_ogar_1636, retro_ogar_2241, retro_ogar_2361, retro_ogar_269, retro_ogar_2775, retro_ogar_3283, retro_ogar_3367, retro_ogar_563, retro_ogar_712, retro_ogar_87,
Procavia capensis	ENSPCAG00000002934	5 retrocopies	retro_pcap_113, retro_pcap_142, retro_pcap_304, retro_pcap_362, retro_pcap_41,
Pan troglodytes	ENSPTRG00000007823	2 retrocopies	retro_ptro_289, retro_ptro_76,
Sarcophilus harrisii	ENSSHAG00000017293	6 retrocopies	retro_shar_311, retro_shar_555, retro_shar_619, retro_shar_720, retro_shar_736, retro_shar_764,
Tarsius syrichta	ENSTSYG00000007627	45 retrocopies	retro_tsyr_1017, retro_tsyr_1024, retro_tsyr_1049, retro_tsyr_1051, retro_tsyr_1151, retro_tsyr_124, retro_tsyr_1240, retro_tsyr_128, retro_tsyr_1336, retro_tsyr_1449, retro_tsyr_1500, retro_tsyr_1517, retro_tsyr_152, retro_tsyr_1562, retro_tsyr_1628, retro_tsyr_1669, retro_tsyr_1808, retro_tsyr_1814, retro_tsyr_184, retro_tsyr_1928, retro_tsyr_1959, retro_tsyr_2041, retro_tsyr_2137, retro_tsyr_2145, retro_tsyr_2164, retro_tsyr_258, retro_tsyr_271, retro_tsyr_274, retro_tsyr_275, retro_tsyr_284, retro_tsyr_289, retro_tsyr_292, retro_tsyr_332, retro_tsyr_420, retro_tsyr_422, retro_tsyr_449, retro_tsyr_538, retro_tsyr_588, retro_tsyr_595, retro_tsyr_630, retro_tsyr_631, retro_tsyr_68, retro_tsyr_687, retro_tsyr_72, retro_tsyr_79,