RetrogeneDB ID: retro_mmus_1043

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:81064683..81065800(+)
• Located in intron of: ENSMUSG00000097098

Retrocopy information

• Ensembl ID: ENSMUSG00000043889
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Actg1
• Ensembl ID: ENSMUSG00000062825
• Aliases: Actg1, AL023024, Actg, Actl, E51
• Description: actin, gamma, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:87906]

Sequence

>retro_mmus_1043
ATGGAAGAAGAAATTGCCGCACTCGTCATTGACAATGGCTCCGGCATGTGCAAAGCCGGCTTTGCTGGCGACGACGCCCC
CAGGGCCGTGTTCCCTTCCATCGTAGGGCGCCCCCGACACCAGGGCGTCATGGTGGGCATGGGCCAGAAAGACTCGTACG
TGGGTGACGAGGCCCAGAGCAAGAGGGGTATCCTGACCCTGAAGTACCCTATCGAACACGGCATTGTCACTAACTGGGAC
GACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTGCGTGTGGCTCCTGAGGAGCACCCGGTGCGAGGCCCCCC
TGAACCCCAAAGCTAACAGAGAGAAGATGACGCAGATAATGTTTGAAACCTTCAATACCCCAGCCATGTACGTGGCCATT
CAGGCGGTGCTGTCCTTGTATGCATCTGGGCGCACCACTGGCATTGTCATGGACTCTGGTGACAGGGTCACACACACAGT
GCCCATCTATGAGGGCTACGCCCTTCCCCACGCCATCTTGCGTCTGGACCTGGCTGGCCGGGACCTGACAGACTACCTCA
TGAAGATCCTGACTGAACGGGGCTACAGCTTTACCACCACTGCTGAAAGGGAAATTGTTCGTGACATAAAGGAGAAGCTG
TGCTATGTTGCCCTGGATTTTGAGCAAGAAATGGCTACTGCTGCATCATCTTCCTCCTTGGAGAAGAGTTACAAGCTGCC
CGACGGGCAGGTGATCACCATTGGCAATGAGCGGTTCCGTTGTCCGGAGGCACTCTTCCAGCCTTCCTTCCTGGGCATGG
AGTCCTGTGGTATCCATGAGACCACTTTCAACTCCATCATGAAGTGTGATGTGGATATCTGCAAAGACCTGTATGCCAAT
ACAGTGCTGTCTGGTGGTACCACCATGTACCCAGGCATTGCTGACAGGATGCAGAAGGAGATCACAGCCCTAGCACCTAG
CACGATGAAGATTAAGATCATTGCTCCCCCTGAGCGCAAGTACTCAGTCTGGATCGGTGGCTCCATTCTGGCCTCACTGT
CCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGATGAGTCGGGCCCCTCCATCGTCCACCGCAAATGCTTC

Alignment

ORF - retro_mmus_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
Retrocopy MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPK-ANREKMTQIMFETFNTPAMYVAIQAV
          IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPV.....P..P..ANREKMTQIMFETFNTPAMYVAIQAV
Retrocopy IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPV---RGPPEPQ>ANREKMTQIMFETFNTPAMYVAIQAV

Parental  LSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
          LSLYASGRTTGIVMDSGD.VTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
Retrocopy LSLYASGRTTGIVMDSGDRVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV

Parental  RDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
          RDIKEKLCYVALDFEQEMATAASSSSLEKSY.LPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
Retrocopy RDIKEKLCYVALDFEQEMATAASSSSLEKSYKLPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF

Parental  NSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
          NSIMKCDVDI.KDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
Retrocopy NSIMKCDVDICKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL

Parental  STFQQMWISKQEYDESGPSIVHRKCF
          STFQQMWISKQEYDESGPSIVHRKCF
Retrocopy STFQQMWISKQEYDESGPSIVHRKCF

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	0.26 RPM	87.12 RPM
SRP007412_cerebellum	0.22 RPM	43.55 RPM
SRP007412_heart	0.25 RPM	49.59 RPM
SRP007412_kidney	0.37 RPM	94.88 RPM
SRP007412_liver	0.00 RPM	11.31 RPM
SRP007412_testis	0.37 RPM	97.38 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1043 was not detected

EST

No EST(s) were mapped for retro_mmus_1043 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_31239	121 libraries	178 libraries	574 libraries	182 libraries	17 libraries

The graphical summary, for retro_mmus_1043 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_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1043 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000025228	1 retrocopy	retro_mmus_2686,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043 , retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,