RetrogeneDB ID: retro_mmus_22

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:24476501..24477356(-)
• Located in intron of: ENSMUSG00000024867

Retrocopy information

• Ensembl ID: ENSMUSG00000074922
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fam122b
• Ensembl ID: ENSMUSG00000036022
• Aliases: Fam122b, 4632404H22Rik, AI256344, SPACIA2
• Description: family with sequence similarity 122, member B [Source:MGI Symbol;Acc:MGI:1926005]

Sequence

>retro_mmus_22
ATGGCTCAGGAGAAGATGGAGCTGGACCTGGAGTTGCCCGCGGGCGCGAGCCCGGCGGAGGGCGGCGGCCCTGGCGGCGG
GGGCCTGCGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGCGACTCGTCGCCGGTGTTCCAGGCCGAGGCGCCCA
GCGCCAGACGGAACAGCACGACGTTCCCGAGCCGCCACGGCCTGCTGCTCCCGGCCTCGCCGGTCCGAATGCACAGCAGC
CGCCTGCACCAGATCAAACAGGAGGAGGGCATGGACCTGATCAACCGAGAGACCGTTCACGAGCGCGAGGTGCAGACCGC
AATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCCCGAAGCGCA
TCGATTTCATTCCGGTGTCTCCGGCACCGTCCCCGACCCGGGGAATTGGGAAGCAGTGTTTCTCACCGTCCTTGCAAAGT
TTTGTGAGTAGCAACGGACTGCCTCCAAGTCCCATTCCCAGCCCAACCACCCGATTTACCACCCGGAGAAGCCAGAGTCC
CATCAACTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGATTATCAGCCAAAGAGAT
TTTTCCAGGGCATCACCAACATGCTGTCTTCTGACGTTGCACAGCTGTCAGACCCCGGTGTGTGCGTATCTTCCGATACC
CTGGATGGAAACAGCAGCAGTGCCGGATCTTCCTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTCTCCTGTGTC
GCCCGCCCAAGCAGCCTCCCCCTTTATTCCAGTAGATGAACTTTCCTCAAAGTGA

Alignment

ORF - retro_mmus_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.5 %
• Parental protein coverage: 76.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEGLDMMNRETTNEREAQAGMQISQSWDESLSLSDSDFDKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCL
          EEG.D..NRET..ERE.Q..MQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQC.
Retrocopy EEGMDLINRETVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCF

Parental  SPSLQMFVSSSGMPPSPVLNP-RHFSSRRSQSPVKCIRPSVLGPLKRKGEMEMESQPKRPFQGTTSMLST
          SPSLQ.FVSS.G.PPSP...P...F..RRSQSP..CIRPSVLGPLKRK.EME...QPKR.FQG.T.MLS.
Retrocopy SPSLQSFVSSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETDYQPKRFFQGITNMLSS

Parental  NPAQLSDFSSC--SDILDGSSISSGLSSDSLATGSAPAESPVACSNSCSPFILMDDLSPK
          ..AQLSD...C..SD.LDG.S.S.G.S..S.A..S....SPV......SPFI..D.LS.K
Retrocopy DVAQLSDPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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	6.59 RPM	5.37 RPM
SRP007412_cerebellum	7.34 RPM	4.56 RPM
SRP007412_heart	11.89 RPM	4.51 RPM
SRP007412_kidney	9.70 RPM	7.47 RPM
SRP007412_liver	6.31 RPM	3.00 RPM
SRP007412_testis	8.23 RPM	2.88 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_22 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	19:24476947..24477763
ENCFF001YIJ	POLR2A	19:24476454..24479066
ENCFF001YKA	POLR2A	19:24474297..24479094

EST

No EST(s) were mapped for retro_mmus_22 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_63200	6 libraries	0 libraries	6 libraries	40 libraries	1020 libraries
TSS #2	TSS_63202	1062 libraries	6 libraries	3 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_22 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_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_22 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_35
Rattus norvegicus	retro_rnor_651
Oryctolagus cuniculus	retro_ocun_205
Bos taurus	retro_btau_103
Canis familiaris	retro_cfam_181
Equus caballus	retro_ecab_91

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22 ,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,