RetrogeneDB ID: retro_mmus_1148

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:115528555..115529772(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl3
• Ensembl ID: ENSMUSG00000060036
• Aliases: Rpl3, F2, J1
• Description: ribosomal protein L3 [Source:MGI Symbol;Acc:MGI:1351605]

Sequence

>retro_mmus_1148
ATGTCTCACAGGAAATTCTCAGTTCCCAGGCATGGGTCCTTGGGCTTCCTGCCTCGCAAGCGCAGCAGCAGGCATCATGG
GAAAGTGAAGAGCTTTCCTAAGGATGACGCTTCCAAGCCTGTTCACCTCACAGCCTTTCTGGGTTACAAGGCTGGCATGA
CCCACATCGTCCGGGAAGTTGGCAGGCCAGGATCTAAGGTGAACAAGAAAGAAGTCGTGGAGGCTGTGACCATTGTGGAA
CCCCCCACCCCCACCCAGTGATGGTTGTGGGCATTGTGGGATATGTTGAGACCCCACGAGGCCTCCGGACCTTCAAGACT
GTATTTGCTGAGCACATCAGCGATGAGTGTAAAAGGCGCTTCTATAAGAACTGGCACAAGTCTAAGAAGAAGGCTTTCAC
CAAGTACTGTAAGAAATGGCAGGATGACACAGGCAAGAAGCAGCTGGAGAAGGACTTCAACAGCATGAAGAAGTACTGCC
AGGTCATCCGCATCATTGCCCACACTCAGATGCGTCTGCTTCCTCTGCGCCAGAAGAAGGCACACTTGATGGAGATCCAG
GTGAATGGGGGCACTGTGGCTGAGAAGCTCGACTGGGCCTGAGAGAGGCTGGAGCAGCAGGTTCCTGTGAACCAGGTGTT
TGGGCAGGATGAGGTGATTGATGTCATCGGCGTGACAAAAGGCAAAGGGTACAAAGGGTTAACCAGTCGTTGGCATACAA
AGAAACTGCCCTGAAAGACCCATCGAGGTTTGCGCAAAGTTGCCTGTATTGGAGCCTGGCACCATGCCCGTATCGCCTTC
TCTGTGGCTCGAGCTGGGCAGAAAGGCTACCATCACCGAACAGAGATTAACAATAAGATTTACAAGATTGGTCAAGGCTA
CCTCATCAAGGATGGCAAACAGATCAAGAACAATGCATCTACTGACTATGACTTGTCTGACAAGAGCATCAACCCACTGG
GTGGCTTTGTCCATTATGGTGAGGTGACCAATGACTTCATCATGCTCAAAGGCTGTGTGGTGGGGACCAAGAAGCGAGTA
CTTACACTTCGTAAGTCCTTGCTGGTCCAGACCAAACGTCGGGCCCTGGAGAAGATTGACCTGAAGTTCATTGACACCAC
CTCCAAATTTGGCCATGGTCACTTCCAGACCATGGAGGAGAAGAAAGCATTTATGGGACCACTCAATAAAGATAGCATTG
CCAAGGAGGAAGGAGCT

Alignment

ORF - retro_mmus_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
          MSHRKFS.PRHGSLGFLPRKRSSRH.GKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREV.RPGSKVNKK
Retrocopy MSHRKFSVPRHGSLGFLPRKRSSRHHGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVGRPGSKVNKK

Parental  EVVEAVTIVE-TP---PMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKK
          EVVEAVTIVE.TP...P..VVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKK
Retrocopy EVVEAVTIVE<TPHPHPVMVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKK

Parental  WQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVP
          WQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWA.ERLEQQVP
Retrocopy WQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWA*ERLEQQVP

Parental  VNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHH
          VNQVFGQDE.IDVIGVTKGKGYKG.TSRWHTKKLP.KTHRGLRKVACIGAWH.AR.AFSVARAGQKGYHH
Retrocopy VNQVFGQDEVIDVIGVTKGKGYKGLTSRWHTKKLP*KTHRGLRKVACIGAWHHARIAFSVARAGQKGYHH

Parental  RTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLT
          RTEIN.KIYKIGQGYLIKDGK.IKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLT
Retrocopy RTEINNKIYKIGQGYLIKDGKQIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLT

Parental  LRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
          LRKSLLVQTKRRALEKIDLKFIDTTSKFGHG.FQTMEEKKAFMGPL.KD.IAKEEGA
Retrocopy LRKSLLVQTKRRALEKIDLKFIDTTSKFGHGHFQTMEEKKAFMGPLNKDSIAKEEGA

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	0.14 RPM	182.07 RPM
SRP007412_cerebellum	0.04 RPM	112.33 RPM
SRP007412_heart	0.06 RPM	83.24 RPM
SRP007412_kidney	0.10 RPM	150.53 RPM
SRP007412_liver	0.03 RPM	142.14 RPM
SRP007412_testis	0.09 RPM	55.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1148 was not detected

EST

No EST(s) were mapped for retro_mmus_1148 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_26881	157 libraries	375 libraries	496 libraries	40 libraries	4 libraries

The graphical summary, for retro_mmus_1148 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 131 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010853	1 retrocopy	retro_amel_1115,
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Callithrix jacchus	ENSCJAG00000016276	6 retrocopies	retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus	ENSDNOG00000001121	4 retrocopies	retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Erinaceus europaeus	ENSEEUG00000014661	2 retrocopies	retro_eeur_488, retro_eeur_557,
Echinops telfairi	ENSETEG00000011380	5 retrocopies	retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus	ENSFCAG00000005820	1 retrocopy	retro_fcat_1809,
Gorilla gorilla	ENSGGOG00000002326	10 retrocopies	retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Myotis lucifugus	ENSMLUG00000023711	1 retrocopy	retro_mluc_810,
Macaca mulatta	ENSMMUG00000010029	4 retrocopies	retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Mustela putorius furo	ENSMPUG00000013271	3 retrocopies	retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Mus musculus	ENSMUSG00000060036	30 retrocopies	retro_mmus_1148 , retro_mmus_1158, retro_mmus_1164, retro_mmus_1165, retro_mmus_1167, retro_mmus_1183, retro_mmus_1238, retro_mmus_1239, retro_mmus_1240, retro_mmus_1241, retro_mmus_1242, retro_mmus_1243, retro_mmus_1244, retro_mmus_1245, retro_mmus_1246, retro_mmus_1465, retro_mmus_1548, retro_mmus_2231, retro_mmus_2275, retro_mmus_2276, retro_mmus_2474, retro_mmus_2501, retro_mmus_2547, retro_mmus_2849, retro_mmus_3125, retro_mmus_3215, retro_mmus_3422, retro_mmus_3467, retro_mmus_361, retro_mmus_897,
Oryctolagus cuniculus	ENSOCUG00000027712	4 retrocopies	retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii	ENSOGAG00000000032	7 retrocopies	retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps	ENSOPRG00000013088	3 retrocopies	retro_opri_1004, retro_opri_1014, retro_opri_432,
Procavia capensis	ENSPCAG00000010642	1 retrocopy	retro_pcap_115,
Pongo abelii	ENSPPYG00000011837	10 retrocopies	retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pteropus vampyrus	ENSPVAG00000003204	2 retrocopies	retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus	ENSRNOG00000016896	2 retrocopies	retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii	ENSSHAG00000003212	2 retrocopies	retro_shar_154, retro_shar_662,
Tupaia belangeri	ENSTBEG00000005989	1 retrocopy	retro_tbel_939,