RetrogeneDB ID: retro_mmus_428

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:33108909..33109657(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Fam192a
• Ensembl ID: ENSMUSG00000031774
• Aliases: Fam192a, 1700001O11Rik, 2310065K24Rik, AI596259, Nip30
• Description: family with sequence similarity 192, member A [Source:MGI Symbol;Acc:MGI:1919637]

Sequence

>retro_mmus_428
ATGGATGGAGAGAACGATGTTAACCTTGTCACCAAAGAGAGGTTTGTGTCTGAGGCAGAACTAGACAAGCCATGCAAAGG
GAGGCAAGAAGAATAGGAGAAAGTGTGGAAACCAGAAGAACCAGAAGAATGTCCAGAGGAGGCCTGTGACCCTTGGTCTT
TGTATGAACCGCTGAAGGAACAAAAAGACAGGAAGCAGCAGTATGAGGAGCAAGCAGTTTAAATTCAAAAACATGGCAAG
AGGGTTAGATGAAGATGAGACCAACTTCCTTGATGAGGTTTCTCAGCAGCAGGAGCTGATTGAGAAGCAGCGAAAAGAAG
AACTGGAGGATCTGAAGGAGTACAAAAGGAATCACAACAAGGTTGGGATTTCTGCAGAAAATAAGGAAGTAGAGAAGAAG
CTGGCTGTGAAACCCATAGAAACCAAGAACAAGTTCTCCCAGGCAAAGCTGTTGGCAGGAGCTGTGAAGCTGAACAGCTC
AGAGAGTGGCAATAGTGTGAAAAGACTGAAACCAGACTCCGACCCGGATGACAGGGCTCAAGAGGCCCCATCCTGCATGT
CTCTTGGAAGCCCTTTTCTGAGCGGACCTCCCTCCATTCACTGCCCATCTGCTGCTATGTGAACCGGCATCCTCCCTGGC
TTGGGCACCTGTTCTGGGAGCAGTGACTCTGAATTCAGTTCAGACAGTGAAGGCACCATCAATGCTACAGGGAAGATCGT
CTCCTCCATCTTCCAAACCAACACCTTC

Alignment

ORF - retro_mmus_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDGEDDSNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPKECPEEAYDPRSLYERLQEQKDRKQQEYE
          MDGE.D.NLV.K.RFVSEAELD...K.RQEE.EKV........CPEEA.DP.SLYE.L.EQKDRKQQ..E
Retrocopy MDGENDVNLVTKERFVSEAELDKPCKGRQEE*EKVWXXXXXXXCPEEACDPWSLYEPLKEQKDRKQQYEE

Parental  E-QFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELEELKEYRSNLNKVGISAENKEVEKKLAVKP
          ..QFKFKNM.RGLDEDETNFLDEVS.QQELIEKQR.EE.LE.LKEY..N.NKVGISAENKEVEKKLAVKP
Retrocopy Q>QFKFKNMARGLDEDETNFLDEVSQQQELIEKQRKEE-LEDLKEYKRNHNKVGISAENKEVEKKLAVKP

Parental  IETKNKFSQAKLLAGAVKHKSSESGNSVKRLKPDPDPDDKAQEAPSCMSLGSSSLSGPPSIHCPSAAVCI
          IETKNKFSQAKLLAGAVK..SSESGNSVKRLKPD.DPDD.AQEAPSCMSLGS..LSGPPSIHCPSAA...
Retrocopy IETKNKFSQAKLLAGAVKLNSSESGNSVKRLKPDSDPDDRAQEAPSCMSLGSPFLSGPPSIHCPSAAM*T

Parental  GILPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTF
          GILPGLG..SGSSDSE.SSDSEGTINATGKIVSSIF.TNTF
Retrocopy GILPGLGTCSGSSDSEFSSDSEGTINATGKIVSSIFQTNTF

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	0.02 RPM	33.08 RPM
SRP007412_cerebellum	0.00 RPM	42.55 RPM
SRP007412_heart	0.00 RPM	19.74 RPM
SRP007412_kidney	0.02 RPM	28.59 RPM
SRP007412_liver	0.03 RPM	21.52 RPM
SRP007412_testis	0.00 RPM	42.45 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_428 was not detected

EST

No EST(s) were mapped for retro_mmus_428 retrocopy.

TSS

No TSS is located nearby retro_mmus_428 retrocopy 5' end.

Lab

retro_mmus_428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428 ,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,