RetrogeneDB ID: retro_mmus_2509

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:119334677..119335445(-)
• Located in intron of: ENSMUSG00000028637

Retrocopy information

• Ensembl ID: ENSMUSG00000083836
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ldhb
• Ensembl ID: ENSMUSG00000030246
• Aliases: Ldhb, AI790582, H-Ldh, LDH-B, LDH-H, Ldh-2, Ldh2
• Description: lactate dehydrogenase B [Source:MGI Symbol;Acc:MGI:96763]

Sequence

>retro_mmus_2509
ATGGCAACCCTCAAGGACCAGCTGATTGTGAATCTTCTTAAGGAAGAGCAGGCTCCCCAGGACAAGATTACAGTTGTTGG
GGTTGGTGCTGTTGGCATGGCTTGTGCCATCAGTATCTTAATGAAGGGCTTGGCGGATGAGCTTGCCCTTGTTGACGTCA
TGGAAGACAAACTCAAGGGCGAGATGATGGATCTCCAGCATGGCAGCCTCTTCCTTAAAACACCAAAAATTGTCTTCAGC
AAAGACTACTGTGTAACTGCGAACGCCAAGCTGGTCATCATCACAGGGGTGTCTGTCAGCAAGAGGGGGAGAGCCAACTC
AACCTGGTCCAACGAAACATGAACATCTTCAAGTTCATCACTGCCAACATTGTGAAGCACAGTCCACACTTCGAGCTGCT
GATTGTCTCAAATCCAGTGGATATCTTGACCTACGTGGCTTGGAAAATCAGTGGCTTTCCCAAAAGCCGAGTTATTGGAA
GTGGTTGCAGTCTGGATTCAGCTCGGTTCTGTTACCTGATGGAAGAAAGGCTGGGGGTTCACCCTGAGCTGTCATGGCTG
GGTCCTGGGAGAACATGGCAACTCCAGTGTGCCTGTGTGGAATGGTGTGAACGTTGCCGGTGTCTCCCTGAAGTCTCTGA
ACCCAGAACTGGGCACTGATGCAGACAAGGAACAGTGGAAGGAGGTTCAAAAGCAGGTGGTGGACAGTGCCTCCAAGGTG
ATCAAGCTGAGAGGTTACACATCCTGGGCCATTGGCCTCTCTGTGGCA

Alignment

ORF - retro_mmus_2509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 77.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIASVADDEAAVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
          MATLK..LI......E.A.P..KITVVGVG.VGMACAISIL.K.LADELALVDV.EDKLKGEMMDLQHGS
Retrocopy MATLKDQLIVNLLKEEQA-PQDKITVVGVGAVGMACAISILMKGLADELALVDVMEDKLKGEMMDLQHGS

Parental  LFLQTPKIVADKDYSVTANSKIVVVTA-GVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCTIIVVSN
          LFL.TPKIV..KDY.VTAN.K.V..T..GV.QQEGES.LNLVQRN.N.FKFI...IVK.SP......VSN
Retrocopy LFLKTPKIVFSKDYCVTANAKLVIITG<GVCQQEGESQLNLVQRNMNIFKFITANIVKHSPHFELLIVSN

Parental  PVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAE-KLGIHP-SSCHGWILGEHGDSSVAVWSGVNV
          PVDILTYV.WK.SG.PK.RVIGSGC.LDSARF.YLM.E.K.G..P..SCHGW.LGEHG.SSV.VW.GVNV
Retrocopy PVDILTYVAWKISGFPKSRVIGSGCSLDSARFCYLMEE<KAGGSP<LSCHGWVLGEHGNSSVPVWNGVNV

Parental  AGVSLQELNPEMGTDNDSENWKEVHKMVVDSAYEVIKLKGYTNWAIGLSVA
          AGVSL..LNPE.GTD.D.E.WKEV.K.VVDSA..VIKL.GYT.WAIGLSVA
Retrocopy AGVSLKSLNPELGTDADKEQWKEVQKQVVDSASKVIKLRGYTSWAIGLSVA

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	0.21 RPM	323.16 RPM
SRP007412_cerebellum	0.13 RPM	420.62 RPM
SRP007412_heart	0.34 RPM	1199.98 RPM
SRP007412_kidney	0.21 RPM	997.84 RPM
SRP007412_liver	0.14 RPM	2.65 RPM
SRP007412_testis	0.64 RPM	63.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2509 was not detected

EST

No EST(s) were mapped for retro_mmus_2509 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_99902	448 libraries	531 libraries	91 libraries	0 libraries	2 libraries

The graphical summary, for retro_mmus_2509 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_2509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2509 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
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,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,