RetrogeneDB ID: retro_mmus_1608

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:5417511..5418513(-)
• Located in intron of: ENSMUSG00000004945

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ldha
• Ensembl ID: ENSMUSG00000063229
• Aliases: Ldha, Ldh1, Ldhm, l7R2
• Description: lactate dehydrogenase A [Source:MGI Symbol;Acc:MGI:96759]

Sequence

>retro_mmus_1608
TCCTCCATGGCGACCGTGAAGGGTGAACTTATCCAGCACATCAGCTCCGAAGAGCCCGTTCTCCACAACAAGGTCTCCAT
TGTAGGAACTGGATCAGTCGGCATGGCCTGTGCCATCGGCATCATAGCGAAAGGCTTGACTGACGAGCTCGCCCTTGTTG
ATAATAATGAAGAAAAAATGAAGGGTGAGACGATGGATCTTCAGCACGGCAGTGTCTTCATGAAAATGCCAAATATTGTT
TGCAGCAAGGATTTCCGTGTCACTGCCAACTCTGAGGTAGTGATTATCACAGCGGGTGCACGCCAAGAGAAAAATGAGAC
ACGCCTGAATTTAGTCCAGCGAAACGTAACCATCTTTAAGGCAATGGTTGCGGAAATTATCAAGCACAGCCCTCGCTGCA
AAATTATTGTTGTCTCCAATCCAGTGGATATCTTAACTTTCGTAACCTGGAAGTTGAGTGGGTTTCCCAAAAACCGTATT
ATTGGAAGCGGCTGTAACCTAGATACAGCTCGCTTCCGTTACATGCTCGGGCAGAGGCTTGGGATCCACTCTGAAAGCTG
CCACGGGTGGGTCCTTGGAGAGCATGGAGATTCAAGTGTCCCTGTGTGGAGTGGTGTGAACATCGCCGGCGTGCCGCTGA
GAGAGCTGAATTCAGCTATAGGAACAAGCAAAGACCCCGAGAAATGGGGCGATGTCCACAAAGAAGTCATTGCCAGTGCC
TATAATATTATCAAAATGAAAGGTTATACTTCCTGGGCCATTGGCCTGTCTGTAACTGATATTGCAGAGAGTATCCTGAA
GAATCTCAGGAAGACGCATCCAGTTACCACCAAAATCCAAGGTCTCTACGGAATCAAAGAGGAGGTGTTCCTCAGCGTGC
CTTGTATCCTGGGAGAGAGTGGCATATCTGATATCATAAAGGTAAAGCTGAGCCCTACAGAGGAGGCCCAGATGGTAAAG
AGCGCAGAGACTATTTGGAAAATCCAGAAAGATATTAAGTTT

Alignment

ORF - retro_mmus_1608 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.07 %
• Parental protein coverage: 92.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKMATLKDQLIVNLLKEEQAPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHG
          S.MAT.K..LI.....EE....NK...VG.G.VGMACAI.I..K.L.DELALVD..E.K.KGE.MDLQHG
Retrocopy SSMATVKGELIQHISSEEPVLHNKVSIVGTGSVGMACAIGIIAKGLTDELALVDNNEEKMKGETMDLQHG

Parental  SLFLKTPKIVSSKDYCVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPHCKLLIVSN
          S.F.K.P.IV.SKD..VTANS..VIITAGARQ...E.RLNLVQRNV.IFK.....I.K.SP.CK...VSN
Retrocopy SVFMKMPNIVCSKDFRVTANSEVVIITAGARQEKNETRLNLVQRNVTIFKAMVAEIIKHSPRCKIIVVSN

Parental  PVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWVLGEHGDSSVPVWSGVNVAG
          PVDILT.V.WK.SGFPKNR.IGSGCNLD.ARFRY..G.RLG.H..SCHGWVLGEHGDSSVPVWSGVN.AG
Retrocopy PVDILTFVTWKLSGFPKNRIIGSGCNLDTARFRYMLGQRLGIHSESCHGWVLGEHGDSSVPVWSGVNIAG

Parental  VSLKSLNPELGTDADKEQWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIK
          V.L..LN...GT..D.E.W..VHK.V..SAY..IK.KGYTSWAIGLSV.D.AESI.KNLR..HP..T.I.
Retrocopy VPLRELNSAIGTSKDPEKWGDVHKEVIASAYNIIKMKGYTSWAIGLSVTDIAESILKNLRKTHPVTTKIQ

Parental  GLYGINEDVFLSVPCILGQNGISDVVKVTLTPEEEARLKKSADTLWGIQKELQF
          GLYGI.E.VFLSVPCILG..GISD..KV.L.P.EEA...KSA.T.W.IQK...F
Retrocopy GLYGIKEEVFLSVPCILGESGISDIIKVKLSPTEEAQMVKSAETIWKIQKDIKF

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	0.23 RPM	162.35 RPM
SRP007412_cerebellum	0.39 RPM	72.30 RPM
SRP007412_heart	0.06 RPM	465.65 RPM
SRP007412_kidney	0.31 RPM	344.67 RPM
SRP007412_liver	0.19 RPM	394.74 RPM
SRP007412_testis	439.09 RPM	722.17 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1608 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YJZ	POLR2A	17:5408855..5419001
ENCFF001YKA	POLR2A	17:5419049..5419312
ENCFF001YKA	POLR2A	17:5418449..5418670

EST

No EST(s) were mapped for retro_mmus_1608 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_55298	1018 libraries	42 libraries	6 libraries	0 libraries	6 libraries

The graphical summary, for retro_mmus_1608 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

• Experiment type: PCR amplification
• Forward primer: GCAGAAGAGTGAGTACAACC (20 nt long)
• Reverse primer: CACACTTATGAAAGTTAGCCG (21 nt long)
• Annealing temperature: 55 °C
• (Expected) product size: 1362
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1608 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_578

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 226 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017854	2 retrocopies	retro_amel_389, retro_amel_462,
Bos taurus	ENSBTAG00000008683	2 retrocopies	retro_btau_1715, retro_btau_1822,
Choloepus hoffmanni	ENSCHOG00000009977	14 retrocopies	retro_chof_1038, retro_chof_144, retro_chof_1489, retro_chof_1524, retro_chof_1547, retro_chof_172, retro_chof_1874, retro_chof_2121, retro_chof_217, retro_chof_2365, retro_chof_2588, retro_chof_2611, retro_chof_552, retro_chof_990,
Callithrix jacchus	ENSCJAG00000007094	1 retrocopy	retro_cjac_2290,
Cavia porcellus	ENSCPOG00000011926	2 retrocopies	retro_cpor_1055, retro_cpor_427,
Dasypus novemcinctus	ENSDNOG00000018915	11 retrocopies	retro_dnov_1063, retro_dnov_1366, retro_dnov_1429, retro_dnov_1707, retro_dnov_1848, retro_dnov_2417, retro_dnov_362, retro_dnov_669, retro_dnov_797, retro_dnov_821, retro_dnov_887,
Equus caballus	ENSECAG00000020669	5 retrocopies	retro_ecab_1004, retro_ecab_765, retro_ecab_837, retro_ecab_924, retro_ecab_933,
Echinops telfairi	ENSETEG00000007508	15 retrocopies	retro_etel_1091, retro_etel_1192, retro_etel_1243, retro_etel_1309, retro_etel_1439, retro_etel_1609, retro_etel_1870, retro_etel_1916, retro_etel_1969, retro_etel_1996, retro_etel_2209, retro_etel_361, retro_etel_392, retro_etel_828, retro_etel_884,
Homo sapiens	ENSG00000134333	5 retrocopies	retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
Gorilla gorilla	ENSGGOG00000010350	3 retrocopies	retro_ggor_1698, retro_ggor_349, retro_ggor_619,
Loxodonta africana	ENSLAFG00000011307	1 retrocopy	retro_lafr_11,
Macropus eugenii	ENSMEUG00000001462	91 retrocopies	retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
Macaca mulatta	ENSMMUG00000031024	2 retrocopies	retro_mmul_1037, retro_mmul_587,
Monodelphis domestica	ENSMODG00000006522	2 retrocopies	retro_mdom_161, retro_mdom_206,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Mus musculus	ENSMUSG00000043262	1 retrocopy	retro_mmus_907,
Mus musculus	ENSMUSG00000063229	14 retrocopies	retro_mmus_1044, retro_mmus_1300, retro_mmus_1514, retro_mmus_1608 , retro_mmus_1753, retro_mmus_1887, retro_mmus_1889, retro_mmus_1925, retro_mmus_2078, retro_mmus_2592, retro_mmus_2885, retro_mmus_3150, retro_mmus_3694, retro_mmus_497,
Nomascus leucogenys	ENSNLEG00000017767	4 retrocopies	retro_nleu_1037, retro_nleu_1303, retro_nleu_1766, retro_nleu_820,
Oryctolagus cuniculus	ENSOCUG00000015939	6 retrocopies	retro_ocun_1597, retro_ocun_1817, retro_ocun_246, retro_ocun_338, retro_ocun_574, retro_ocun_746,
Pongo abelii	ENSPPYG00000003437	5 retrocopies	retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pan troglodytes	ENSPTRG00000003421	5 retrocopies	retro_ptro_1540, retro_ptro_1618, retro_ptro_2039, retro_ptro_259, retro_ptro_2875,
Rattus norvegicus	ENSRNOG00000013009	17 retrocopies	retro_rnor_1131, retro_rnor_1336, retro_rnor_1738, retro_rnor_1769, retro_rnor_1881, retro_rnor_2146, retro_rnor_2377, retro_rnor_2560, retro_rnor_2830, retro_rnor_2950, retro_rnor_2957, retro_rnor_2984, retro_rnor_490, retro_rnor_491, retro_rnor_563, retro_rnor_578, retro_rnor_843,
Sorex araneus	ENSSARG00000001224	1 retrocopy	retro_sara_657,
Sarcophilus harrisii	ENSSHAG00000015776	1 retrocopy	retro_shar_814,
Sus scrofa	ENSSSCG00000013366	1 retrocopy	retro_sscr_12,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,
Tursiops truncatus	ENSTTRG00000013756	2 retrocopies	retro_ttru_1269, retro_ttru_1802,
Vicugna pacos	ENSVPAG00000010215	5 retrocopies	retro_vpac_175, retro_vpac_222, retro_vpac_237, retro_vpac_629, retro_vpac_79,