RetrogeneDB ID: retro_mmus_755

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:3470904..3471365(-)
• Located in intron of: ENSMUSG00000034587

Retrocopy information

• Ensembl ID: ENSMUSG00000081059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl30
• Ensembl ID: ENSMUSG00000026087
• Aliases: None
• Description: mitochondrial ribosomal protein L30 [Source:MGI Symbol;Acc:MGI:1333820]

Sequence

>retro_mmus_755
TCTGCGCTCCGTGTTCCAGAGGCCTCCATGCAGACTGTGAAGAAAGGTGCAGAATCTCTCATGGTACAGAATAGATTCGT
CACAAATTTACCAAATCAAGAATTCCAGATAAAGTGTTTCAGCCTAAACCTGAAGATCATGAAAAGTACGGTGGGGACCC
CCAGAACCCTCATAAACTGCACATTGTTACAAGAATAAGAAGTACAAAGAGGCGTCCATACTGGGAAAAAGATACCATCA
AGATGCTCGGACTACAGAAGGCACACCGCCCTCAAATTCACAAGAACATCCCATTGGTGAACGCAAAGCTGAAAGTGGTT
AAACACTTGATACGCATCCAGCCCCTGAAGCTGCCACAGGGACTTCCCACAGAAGAGACCATGTCCAGCACGTGCCTCAA
GAGCACGGGGGAGTTGGTCGTGCAGTGACATCTGAAGCCCGTGGAGCAGGAAGTGACGTCC

Alignment

ORF - retro_mmus_755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 96.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SAFPRPPCRLQTVKKGAESLI-GTEWIRHKFTKSRIPDKVFQPKPEDHEKYGGDPQNPHKLHIVTRIRST
          SA...P....QTVKKGAESL..GTE.IRHKFTKSRIPDKVFQPKPEDHEKYGGDPQNPHKLHIVTRIRST
Retrocopy SALRVPEASMQTVKKGAESLM<GTE*IRHKFTKSRIPDKVFQPKPEDHEKYGGDPQNPHKLHIVTRIRST

Parental  KRRPYWEKDTIKMLGLQKAHSPQIHKNIPSVNAKLKVVKHLIRIQPLKLPQGLPTEETMSSTCLKSTGEL
          KRRPYWEKDTIKMLGLQKAH.PQIHKNIP.VNAKLKVVKHLIRIQPLKLPQGLPTEETMSSTCLKSTGEL
Retrocopy KRRPYWEKDTIKMLGLQKAHRPQIHKNIPLVNAKLKVVKHLIRIQPLKLPQGLPTEETMSSTCLKSTGEL

Parental  VVQWHLKPVEQEAKS
          VVQ.HLKPVEQE..S
Retrocopy VVQ*HLKPVEQEVTS

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	30.11 RPM
SRP007412_cerebellum	0.35 RPM	18.71 RPM
SRP007412_heart	0.16 RPM	68.21 RPM
SRP007412_kidney	0.52 RPM	34.23 RPM
SRP007412_liver	0.22 RPM	25.01 RPM
SRP007412_testis	0.64 RPM	19.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_755 was not detected

EST

No EST(s) were mapped for retro_mmus_755 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_12187	75 libraries	20 libraries	589 libraries	319 libraries	69 libraries

The graphical summary, for retro_mmus_755 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_755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_755 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013344	1 retrocopy	retro_amel_1121,
Bos taurus	ENSBTAG00000038949	1 retrocopy	retro_btau_1542,
Canis familiaris	ENSCAFG00000031628	1 retrocopy	retro_cfam_1703,
Choloepus hoffmanni	ENSCHOG00000005804	2 retrocopies	retro_chof_2339, retro_chof_715,
Callithrix jacchus	ENSCJAG00000007085	1 retrocopy	retro_cjac_758,
Dasypus novemcinctus	ENSDNOG00000018648	5 retrocopies	retro_dnov_1430, retro_dnov_1469, retro_dnov_2019, retro_dnov_2348, retro_dnov_571,
Equus caballus	ENSECAG00000015993	1 retrocopy	retro_ecab_309,
Echinops telfairi	ENSETEG00000005006	4 retrocopies	retro_etel_168, retro_etel_2176, retro_etel_232, retro_etel_605,
Felis catus	ENSFCAG00000024233	4 retrocopies	retro_fcat_1430, retro_fcat_196, retro_fcat_528, retro_fcat_669,
Homo sapiens	ENSG00000241962	2 retrocopies	retro_hsap_3476, retro_hsap_981,
Gorilla gorilla	ENSGGOG00000011677	2 retrocopies	retro_ggor_2343, retro_ggor_783,
Microcebus murinus	ENSMICG00000011627	4 retrocopies	retro_mmur_109, retro_mmur_1281, retro_mmur_61, retro_mmur_897,
Myotis lucifugus	ENSMLUG00000029851	2 retrocopies	retro_mluc_1543, retro_mluc_1786,
Mustela putorius furo	ENSMPUG00000011085	1 retrocopy	retro_mputfur_214,
Mus musculus	ENSMUSG00000026087	7 retrocopies	retro_mmus_1171, retro_mmus_1367, retro_mmus_1758, retro_mmus_331, retro_mmus_3680, retro_mmus_3724, retro_mmus_755 ,
Nomascus leucogenys	ENSNLEG00000026974	2 retrocopies	retro_nleu_2761, retro_nleu_337,
Oryctolagus cuniculus	ENSOCUG00000004111	1 retrocopy	retro_ocun_1946,
Otolemur garnettii	ENSOGAG00000002241	11 retrocopies	retro_ogar_1328, retro_ogar_1429, retro_ogar_2160, retro_ogar_2277, retro_ogar_2389, retro_ogar_3516, retro_ogar_401, retro_ogar_466, retro_ogar_549, retro_ogar_879, retro_ogar_908,
Ochotona princeps	ENSOPRG00000007331	2 retrocopies	retro_opri_826, retro_opri_989,
Pan troglodytes	ENSPTRG00000012275	2 retrocopies	retro_ptro_2356, retro_ptro_765,
Pteropus vampyrus	ENSPVAG00000006587	5 retrocopies	retro_pvam_1469, retro_pvam_1484, retro_pvam_321, retro_pvam_432, retro_pvam_764,
Rattus norvegicus	ENSRNOG00000018511	6 retrocopies	retro_rnor_2018, retro_rnor_2683, retro_rnor_2684, retro_rnor_2873, retro_rnor_570, retro_rnor_916,
Rattus norvegicus	ENSRNOG00000049330	1 retrocopy	retro_rnor_2976,
Sus scrofa	ENSSSCG00000008183	2 retrocopies	retro_sscr_529, retro_sscr_555,
Tarsius syrichta	ENSTSYG00000005345	4 retrocopies	retro_tsyr_1736, retro_tsyr_2153, retro_tsyr_368, retro_tsyr_866,
Tursiops truncatus	ENSTTRG00000004937	3 retrocopies	retro_ttru_1126, retro_ttru_1379, retro_ttru_78,