RetrogeneDB ID: retro_mmus_2959

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:101338111..101338426(+)
• Located in intron of: ENSMUSG00000030688

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl31
• Ensembl ID: ENSMUSG00000073702
• Aliases: None
• Description: ribosomal protein L31 [Source:MGI Symbol;Acc:MGI:2149632]

Sequence

>retro_mmus_2959
TTGGGGCCAGCAGAATGGTTCCCGCAAAAAAGGATGGCAAGAAGAAGGGCCATCAACGATGTGGTGACTAGAGAATACAT
CACCAACGTTCACAACCGCATCCATGGAGTGGGCTTCATGAAGCGTGCTCCTTGGGCATTCAAAGAAACCCGGAAATCCT
TCATGAAGGAGATGAGGACTCCAGATGTAAGCATTGACACCAGGCTTAATAAGGCCGTCTGGGCCAAGAGAATAAGGAAT
GTTCCGTATCACATCTGAGTGTGTTTGTTCAGAAAATGTAATGAGGGTGAGGATTCACCAAACAAGCTCTACACA

Alignment

ORF - retro_mmus_2959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 83.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGGEKKKGRS-AINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLN
          ..PA.....K...R..AIN.VVTREY..N.H.RIHGVGF.KRAP.A.KE.RK..MKEM.TPDV.IDTRLN
Retrocopy LGPAEWFPQKRMARRRAINDVVTREYITNVHNRIHGVGFMKRAPWAFKETRKSFMKEMRTPDVSIDTRLN

Parental  KAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYT
          KAVWAK.IRNVPY.I.V.L.RK.NE.EDSPNKLYT
Retrocopy KAVWAKRIRNVPYHI*VCLFRKCNEGEDSPNKLYT

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	0.30 RPM	69.15 RPM
SRP007412_cerebellum	0.35 RPM	44.55 RPM
SRP007412_heart	0.03 RPM	65.62 RPM
SRP007412_kidney	0.40 RPM	77.00 RPM
SRP007412_liver	0.90 RPM	55.14 RPM
SRP007412_testis	0.09 RPM	58.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2959 was not detected

EST

No EST(s) were mapped for retro_mmus_2959 retrocopy.

TSS

No TSS is located nearby retro_mmus_2959 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GGTAAAGTAGGTCAGGCATC (20 nt long)
• Reverse primer: CATACCTAGGCCTTCACACT (20 nt long)
• Annealing temperature: 55 °C
• (Expected) product size: 745
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2959 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019701	9 retrocopies	retro_btau_1043, retro_btau_1100, retro_btau_1553, retro_btau_160, retro_btau_1777, retro_btau_1783, retro_btau_409, retro_btau_524, retro_btau_867,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Microcebus murinus	ENSMICG00000016059	15 retrocopies	retro_mmur_1018, retro_mmur_1028, retro_mmur_1080, retro_mmur_130, retro_mmur_1320, retro_mmur_1369, retro_mmur_1386, retro_mmur_1606, retro_mmur_1617, retro_mmur_476, retro_mmur_506, retro_mmur_538, retro_mmur_639, retro_mmur_796, retro_mmur_996,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Mus musculus	ENSMUSG00000073702	41 retrocopies	retro_mmus_1054, retro_mmus_1143, retro_mmus_1256, retro_mmus_1419, retro_mmus_1456, retro_mmus_1495, retro_mmus_1507, retro_mmus_1532, retro_mmus_1598, retro_mmus_1670, retro_mmus_1674, retro_mmus_1768, retro_mmus_1823, retro_mmus_1836, retro_mmus_1856, retro_mmus_2054, retro_mmus_2152, retro_mmus_2240, retro_mmus_2278, retro_mmus_2398, retro_mmus_2554, retro_mmus_2603, retro_mmus_2620, retro_mmus_2630, retro_mmus_2658, retro_mmus_2677, retro_mmus_2716, retro_mmus_2821, retro_mmus_2959 , retro_mmus_2966, retro_mmus_3186, retro_mmus_3196, retro_mmus_3380, retro_mmus_367, retro_mmus_396, retro_mmus_446, retro_mmus_453, retro_mmus_485, retro_mmus_592, retro_mmus_933, retro_mmus_964,
Oryctolagus cuniculus	ENSOCUG00000002392	9 retrocopies	retro_ocun_1070, retro_ocun_1074, retro_ocun_1161, retro_ocun_117, retro_ocun_1366, retro_ocun_206, retro_ocun_64, retro_ocun_941, retro_ocun_99,