RetrogeneDB ID: retro_mmus_706

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:41498736..41500452(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000058809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hspd1
• Ensembl ID: ENSMUSG00000025980
• Aliases: Hspd1, 60kDa, Hsp60
• Description: heat shock protein 1 (chaperonin) [Source:MGI Symbol;Acc:MGI:96242]

Sequence

>retro_mmus_706
ATGCTTCGACTACCCACAGTCCTTCGCCAGATGAGACCAGTGTCCCGGGCACTGGCTCCTCATCTCACTCGGGCCTATGC
CAAAGATGTAAAATTTGGTGCGGATGCTCGAGCCTTAATGCTTCAAGCTGTAGACCTTTTAGCCGATGCTGTAGCTGTTA
CAATGGGGCCAAAGGGAAGAACTGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTCACTGTT
GCAAAGTCAATTGATTTAAAGGATAAATACAAAAATATTGGAGCTAAACTTGTTCAGGATGTTGCCAATAACACAAACGA
AGAGGCTGGGGATGGCACCACCACTTCCACTGTTCTGGCACGATCTATTGCCAAGGAGGGCTTTGAGAAGATCAGCAAAG
GGGCTAATCCAGTGGAAATCCGGAGAGGTGTGATGTTGGCTGTGGATGCTGTAATTGCTGAACTTAAGAAACAGTCTAAA
CCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGACATTGGGAACATCATTTC
TGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTA
TTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAGGTCAAAAGTGTGAATTCCAA
GATGCCTATGTCTTGTTGAGTGAAAAGAAAATTTCCAGTGTTCAGTCCATTGTCCCTACTCTTGAAATTGCTAATGCTCA
TCGGAAGCCATTGGTCATAATCGCCGAAGACGTTGACGGAGAAGCTCTAAGCACGATGGTTTTGAACAGGCTAAAAGTTG
GTCTTCAGGTTGTGGCAGTCAAAGCTCCAGGATTTGGGGACAATAGGAAGAACCAGCTTAAAGATATGGCTATTGCTACT
GGTGGTGCGGTGTTTGGAGAAGAGGGGTTGAATCTAAATCTTGAAGATGTTCAAGCTCATGACTTAGGAAAAGTTGGGGA
GGTCATTGTCACCAAAGATGATGCCATGCTTTTGAAAGGAAAAGGTGACAAAGCTCACATTGAAAAACGTATTCAAGAAA
TCACTGAGCAGCTAGACATCACAACTAGTGAATATGAAAAGGAAAAGCTGAATGAGCGACTTGCTAAACTTTCAGATGGA
GTAGCTGTGTTGAAGGTTGGAGGAACAAGTGATGTTGAAGTGAATGAAAAAAAAGACAGAGTTACTGACGCTCTCAATGC
TACAAGAGCAGCTGTTGAAGAAGGCATTGTTCTAGGAGGGGGCTGCGCTCTGCTTCGGTGCATCCCAGCCTTGGATTCAT
TAAAGCCTGCTAATGAAGACCAGAAAATAGGTATAGAAATTATTAAAAGAGCACTTAAAATTCCTGCAATGACGATTGCT
AAGAATGCAGGTGTTGAAGGATCTTTGATAGTTGAGAAAATTCTGCAGAGTTCCTCAGAAGTTGGTTATGACGCCAGGCT
TGGAGATTTTGTGAACATGGTGGAAAAAGGGATCATTGATCCAACAAAGGTTGTAAGAACTGCCTTACTGGATGCTGCTG
GAGTGGCCTCCTTGCTAACTACAGCCGAAGCTGTAGTGACAGAAATTCCTAAAGAAGAGAAGGACCCTGGAATGGGTGCA
ATGGGTGGCATGGGAGGGGGTATGGGAGGCAGCATG

Alignment

ORF - retro_mmus_706 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.68 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
          MLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQ.VDLLADAVAVTMGPKGRTVIIEQSWGS
Retrocopy MLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQAVDLLADAVAVTMGPKGRTVIIEQSWGS

Parental  PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
          PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTT.TVLARSIAKEGFEKISKGANPVEI
Retrocopy PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTSTVLARSIAKEGFEKISKGANPVEI

Parental  RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGKTLNDE
          RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGKTLNDE
Retrocopy RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGKTLNDE

Parental  LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDG
          LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVP.LEIANAHRKPLVIIAEDVDG
Retrocopy LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPTLEIANAHRKPLVIIAEDVDG

Parental  EALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGKVGEVIV
          EALST.VLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGKVGEVIV
Retrocopy EALSTMVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGKVGEVIV

Parental  TKDDAMLLKGKGDKAHIEKRIQEITEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDR
          TKDDAMLLKGKGDKAHIEKRIQEITEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVN...DR
Retrocopy TKDDAMLLKGKGDKAHIEKRIQEITEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNXXXDR

Parental  VTDALNATRAAVEEGIVLGGGCALLRCIPALDSLKPANEDQKIGIEIIKRALKIPAMTIAKNAGVEGSLI
          VTDALNATRAAVEEGIVLGGGCALLRCIPALDSLKPANEDQKIGIEIIKRALKIPAMTIAKNAGVEGSLI
Retrocopy VTDALNATRAAVEEGIVLGGGCALLRCIPALDSLKPANEDQKIGIEIIKRALKIPAMTIAKNAGVEGSLI

Parental  VEKILQSSSEVGYDAMLGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEAVVTEIPKEEKDPGMGA
          VEKILQSSSEVGYDA.LGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEAVVTEIPKEEKD.....
Retrocopy VEKILQSSSEVGYDARLGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEAVVTEIPKEEKDXXXXX

Parental  MGGMGGGMGGGM
          .....GGMGG.M
Retrocopy XXXXXGGMGGSM

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	0.33 RPM	93.17 RPM
SRP007412_cerebellum	0.22 RPM	79.33 RPM
SRP007412_heart	1.37 RPM	210.75 RPM
SRP007412_kidney	1.87 RPM	298.39 RPM
SRP007412_liver	1.07 RPM	313.50 RPM
SRP007412_testis	0.14 RPM	22.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_706 was not detected

EST

1 EST(s) were mapped to retro_mmus_706 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA793425	41499153	41499512	100	358	0	357

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_12549	153 libraries	308 libraries	393 libraries	131 libraries	87 libraries
TSS #2	TSS_12550	187 libraries	237 libraries	496 libraries	80 libraries	72 libraries
TSS #3	TSS_12551	414 libraries	486 libraries	166 libraries	3 libraries	3 libraries

The graphical summary, for retro_mmus_706 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_706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_706 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens	ENSG00000144381	7 retrocopies	retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla	ENSGGOG00000008267	6 retrocopies	retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus	ENSMUSG00000025980	5 retrocopies	retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706 ,
Nomascus leucogenys	ENSNLEG00000006874	7 retrocopies	retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii	ENSPPYG00000013046	5 retrocopies	retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,