RetrogeneDB ID: retro_mmus_700

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:30208921..30209257(+)
• Located in intron of: ENSMUSG00000020315

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps16
• Ensembl ID: ENSMUSG00000037563
• Aliases: Rps16, AA420385, AI317031
• Description: ribosomal protein S16 [Source:MGI Symbol;Acc:MGI:98118]

Sequence

>retro_mmus_700
ATGCCATTCAAGTGTCCACTGCAGTCTGAGCAGGTCTGAGCCAAGAAGACAGCCATAGTGGTGGTGCACTTCGAAAGGGA
AATGGCCTATTAAGGCAAACTGATGTCCCCTGGAGATGATCAAGCCACTCAGCGTGGTATATGTTCCTGGAGCCCTTCTG
TTTCTGGGCAAGGAGCAGTTTGCTGGTGTGGATATTCGGGTCTATGTGAAGAGTAGTGGTCTTGGGACCCAAATTTATGC
CATCCCATAGCCCATTTCTAAAGCCCTGGTGGCTTATCAAAAATATGTAGATGAGCCTCTAAGAAAGAGATCAAAGATAC
CCTGCCCCTGTTTGAT

Alignment

ORF - retro_mmus_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.03 %
• Parental protein coverage: 79.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPSKGPLQSVQVFGRKKTATAVAHCKR-GNGL-IKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDI
          MP.K.PLQS.QV...KKTA..V.H..R.GNGL.IK.N..PLEMI.P....Y......L.LGKE.FAGVDI
Retrocopy MPFKCPLQSEQV*A-KKTAIVVVHFER<GNGL<IKAN*CPLEMIKPLSVVY-VPGALLFLGKEQFAGVDI

Parental  RVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDE-ASKKEIKDILIQYD
          RV.VK..G...QIYAI...ISKALVA.YQKYVDE.ASKKEIKD.L...D
Retrocopy RVYVKSSGLGTQIYAIP*PISKALVA-YQKYVDE<ASKKEIKDTLPLFD

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	0.02 RPM	27.17 RPM
SRP007412_cerebellum	0.13 RPM	26.83 RPM
SRP007412_heart	0.09 RPM	63.01 RPM
SRP007412_kidney	0.04 RPM	70.40 RPM
SRP007412_liver	0.00 RPM	66.99 RPM
SRP007412_testis	0.41 RPM	33.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_700 was not detected

EST

No EST(s) were mapped for retro_mmus_700 retrocopy.

TSS

No TSS is located nearby retro_mmus_700 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GAATCATGTCACAAGCCTGTC (21 nt long)
• Reverse primer: GTGCACCTTTCATTGATATTAACTG (25 nt long)
• Annealing temperature: 55 °C
• (Expected) product size: 692
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_700 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014176	1 retrocopy	retro_acar_194,
Ailuropoda melanoleuca	ENSAMEG00000008470	8 retrocopies	retro_amel_1105, retro_amel_1143, retro_amel_1463, retro_amel_1790, retro_amel_1865, retro_amel_306, retro_amel_668, retro_amel_840,
Bos taurus	ENSBTAG00000021093	3 retrocopies	retro_btau_1509, retro_btau_167, retro_btau_441,
Callithrix jacchus	ENSCJAG00000014170	6 retrocopies	retro_cjac_2641, retro_cjac_2737, retro_cjac_3019, retro_cjac_885, retro_cjac_905, retro_cjac_949,
Cavia porcellus	ENSCPOG00000011359	3 retrocopies	retro_cpor_1266, retro_cpor_1408, retro_cpor_1515,
Felis catus	ENSFCAG00000010743	4 retrocopies	retro_fcat_1258, retro_fcat_1709, retro_fcat_1806, retro_fcat_1976,
Homo sapiens	ENSG00000105193	11 retrocopies	retro_hsap_118, retro_hsap_1658, retro_hsap_1736, retro_hsap_1977, retro_hsap_2064, retro_hsap_2230, retro_hsap_2327, retro_hsap_3593, retro_hsap_4209, retro_hsap_787, retro_hsap_813,
Gorilla gorilla	ENSGGOG00000014414	10 retrocopies	retro_ggor_110, retro_ggor_1250, retro_ggor_1344, retro_ggor_1664, retro_ggor_1766, retro_ggor_193, retro_ggor_2423, retro_ggor_2819, retro_ggor_652, retro_ggor_667,
Loxodonta africana	ENSLAFG00000001541	1 retrocopy	retro_lafr_1191,
Myotis lucifugus	ENSMLUG00000029089	5 retrocopies	retro_mluc_1906, retro_mluc_2096, retro_mluc_2174, retro_mluc_2529, retro_mluc_481,
Macaca mulatta	ENSMMUG00000019370	8 retrocopies	retro_mmul_1018, retro_mmul_1080, retro_mmul_1175, retro_mmul_1219, retro_mmul_1403, retro_mmul_20, retro_mmul_767, retro_mmul_862,
Monodelphis domestica	ENSMODG00000013545	4 retrocopies	retro_mdom_1668, retro_mdom_1823, retro_mdom_815, retro_mdom_856,
Mustela putorius furo	ENSMPUG00000017722	5 retrocopies	retro_mputfur_283, retro_mputfur_322, retro_mputfur_447, retro_mputfur_701, retro_mputfur_985,
Mus musculus	ENSMUSG00000037563	11 retrocopies	retro_mmus_1780, retro_mmus_2058, retro_mmus_2125, retro_mmus_2697, retro_mmus_2727, retro_mmus_3091, retro_mmus_3173, retro_mmus_3198, retro_mmus_3202, retro_mmus_700 , retro_mmus_771,
Nomascus leucogenys	ENSNLEG00000014388	3 retrocopies	retro_nleu_1266, retro_nleu_248, retro_nleu_46,
Otolemur garnettii	ENSOGAG00000004497	4 retrocopies	retro_ogar_1229, retro_ogar_1309, retro_ogar_1313, retro_ogar_98,
Oreochromis niloticus	ENSONIG00000000006	1 retrocopy	retro_onil_52,
Pelodiscus sinensis	ENSPSIG00000016930	1 retrocopy	retro_psin_55,
Rattus norvegicus	ENSRNOG00000019578	3 retrocopies	retro_rnor_10, retro_rnor_1823, retro_rnor_302,
Sus scrofa	ENSSSCG00000010712	1 retrocopy	retro_sscr_731,
Sus scrofa	ENSSSCG00000020817	3 retrocopies	retro_sscr_478, retro_sscr_5, retro_sscr_723,