RetrogeneDB ID: retro_mmus_153

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:78491581..78493030(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000061062
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hdac1
• Ensembl ID: ENSMUSG00000028800
• Aliases: Hdac1, HD1, Hdac1-ps, MommeD5, RPD3
• Description: histone deacetylase 1 [Source:MGI Symbol;Acc:MGI:108086]

Sequence

>retro_mmus_153
ATGGCGCAGACTCAGGGCACCAAGAGGAAAGTCTGTTACTACTACGACGGGGATGTTGGAAACTACTATTATGGACAAGG
GCACCCCATGAAGCCTCACCGAATCCGCATGACTCACAATTTGCTGCTCAACTATGGTCTCTACCGAAAAATGGAGATCT
ACCGTCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGTGATGACTACATTAAATTCCTGCGTTCTATTCGC
CCAGATAATATGTCTGAATACAGCAAGCAGATGCAGAGATTCAATGTTGGTGAGGACTGTCCGGTGTTTGATGGCTTGTT
TGAGTTCTGTCAGTTGTCCACAGGAGGCTCTGTCGCAAGTGCTGTGAAGCTTAATAAGCAGCAGACGGACATCGCTGTGA
ACTGGGCTGGGGGCCTGCACCATGCAAAGAAGTCTGAAGCATCTGGCTTCTGTTACGTCGATGATATCGTCTTGGCCATC
CCGGAACTGCTAAAGTACCACCAGAGGGTGCTCTATATTGACATTGATATTCACCATGGCGATGGCGTGGAAGAGGCCTT
CTATACTACAGACCGGGTCATGACTGTGTCCTTTCATAAATACGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGACA
TTGGGGCTGGCAAAGGCAAGTACTATGCTGTGAACTACCCACTGCGAGACGGCATTGACGACGAATCCTATGAAGCCACC
TTTAAGCCAGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGTGCAGTGGTCTTACAGTGTGGCTCAGATTCCCTGTC
TGGGGACCGGTTAGGTTGCTTCAATCTGACCATCAAAGGACACGCCAAGTGTGTGGAGTTCGTGAAGAGTTTCAACTTGC
CCATGCTGATGCTGGGAGGAGGTGGCTACACCATCCGGAATGTTGCTCGCTGCTGGACTTACGAAACAGCGGTGGCCCTG
GACACAGAGATCCCTAATGAGCTGCCCTACAACGACTACTTTGAATACTTTGGACCGGATTTCAAGCTTCACATCAGCCC
TTCCAACATGACCAACCAGAACACTAACGAGTACCTGGAGAAGATCAAGCAGCGTCTCTTTGAGAACTTGAGGATGCTGC
CCCATGCCCCTGGGGTCCAGATGCAGGCCATCCCTGAGGATGCCATCCCAGAAGAGAGTGGGGATGAAGATGAGGAGGAC
CCTGACAAACGCATCTCCATCTGCTCCTCTGACAAACGCATTGCCTGTGAGGAAGAGTTCTCGGACTCAGATGAGGAGGG
AGAAGGTGGTCGCAAGAACTCTTCTAACTTCAAAAAAGCCAAAAGAGTTAAAACAGAGGATGAGAAAGAGAAAGATCCTG
AAGAGAAAAAAGAAGTCACAGAAGAAGAGAAAACCAAGGAGGAGAAGCCAGAAGCCAAAGGGGTCAAAGAAGAGGTCAAG
TTGGCCTGA

Alignment

ORF - retro_mmus_153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTKRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
          MAQTQGTKRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
Retrocopy MAQTQGTKRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH
          DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH
Retrocopy DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH

Parental  HAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
          HAKKSEASGFCYV.DIVLAI.ELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
Retrocopy HAKKSEASGFCYVDDIVLAIPELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD

Parental  LRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG
          LRDIGAGKGKYYAVNYPLRDGIDDESYEA.FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG
Retrocopy LRDIGAGKGKYYAVNYPLRDGIDDESYEATFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG

Parental  HAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNM
          HAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNM
Retrocopy HAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNM

Parental  TNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEF
          TNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEF
Retrocopy TNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEF

Parental  SDSDEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA
          SDSDEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA
Retrocopy SDSDEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA

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	0.12 RPM	13.78 RPM
SRP007412_cerebellum	0.30 RPM	12.42 RPM
SRP007412_heart	0.16 RPM	11.83 RPM
SRP007412_kidney	0.50 RPM	19.44 RPM
SRP007412_liver	0.30 RPM	12.59 RPM
SRP007412_testis	1.97 RPM	57.17 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_153 was not detected

EST

18 EST(s) were mapped to retro_mmus_153 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA152793	78491727	78492137	98.3	402	7	394
AA667606	78491568	78491995	99.1	421	4	415
AV476243	78491569	78492037	99.2	464	4	460
BB858701	78491553	78491996	99.1	439	4	435
BB862453	78491550	78491994	99.4	441	3	438
BE692862	78492303	78492653	99.5	348	2	346
BY016919	78491551	78491908	99.8	354	1	353
BY042380	78491551	78491921	99	366	4	362
BY046130	78491555	78491921	99.5	364	2	362
BY056944	78491555	78491920	99.5	363	2	361
BY081419	78491558	78491912	100	354	0	354
BY299679	78491550	78491914	99.5	362	2	360
CA530681	78491563	78492009	99.4	443	3	440
CA533727	78491570	78492059	98.8	483	6	477
CA566160	78491555	78492032	99.2	473	4	469
CJ069514	78491558	78492060	98.7	495	7	488
CJ165808	78491550	78491990	99.1	436	4	432
CK335814	78491564	78492032	99.2	464	4	460

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_56770	454 libraries	110 libraries	366 libraries	129 libraries	13 libraries

The graphical summary, for retro_mmus_153 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_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_153 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153 ,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,