RetrogeneDB ID: retro_mmus_2227

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:14628821..14629240(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam213a
• Ensembl ID: ENSMUSG00000021792
• Aliases: Fam213a, 5730469M10Rik, AU040822, Pamm
• Description: family with sequence similarity 213, member A [Source:MGI Symbol;Acc:MGI:1917814]

Sequence

>retro_mmus_2227
CCAGGCTGCTTCCTCTACTGAGCGGAAGCAGCAGACCTGTCCTTCCTGAAGCTCAAGTCAGACGAGCTATGTGTTCCTCC
CTGCGCTGTGTGAAGGTGCAGGTGGAGAGAGAAGTGAAGGATTTCCAGCCTTATGCCAAAGGGGAAATCTGGAGGAAAAG
GAAAGAATCCTATGGTTCAGAGAGGCGGAAGCTGATGTTCACGGGCCTCATCCATTTGGGTGTGTGGTACAATTCCTTCT
GGGCGTGGATAGGAGATGTCTCTGGACACCTGGAAGGCGAAGGCTTCATCCTCAGTTTTTGTATAAGATCTGGAAATCAG
GGCATTCTTCTTGAGCACGGAAAAGAAGAATTTGGGGACAGAGTGAACCCACTCTGTTCTGGAGCTGGAAAGAACATCAA
GGCACAGACTCCAGCCTCA

Alignment

ORF - retro_mmus_2227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.28 %
• Parental protein coverage: 62.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGCFLCRAEAADLMSLKPKLDELGVPLYAV-VKEQVKREVEDFQPYFKGEIFLDEKKKFYGPERRKMMFM
          PGCFL..AEAADL..LK.K.DEL.VP..AV.VK.QV.REV.DFQPY.KGEI.....K..YG.ERRK.MF.
Retrocopy PGCFLY*AEAADLSFLKLKSDELCVPPCAV<VKVQVEREVKDFQPYAKGEIWR-KRKESYGSERRKLMFT

Parental  GLIRLGVWYNSFRAWNGGFSGNLEGEGFILGGVFVIGSGKQGILLEHREKEFGDRVNPLSVLEAVKKIKL
          GLI.LGVWYNSF.AW.G..SG.LEGEGFIL...F.I.SG.QGILLEH...EFGDRVNPL....A.K.IK.
Retrocopy GLIHLGVWYNSFWAWIGDVSGHLEGEGFILS--FCIRSGNQGILLEHGKEEFGDRVNPL-CSGAGKNIKA

Parental  QTPAS
          QTPAS
Retrocopy QTPAS

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	0.00 RPM	70.51 RPM
SRP007412_cerebellum	0.00 RPM	100.30 RPM
SRP007412_heart	0.00 RPM	15.57 RPM
SRP007412_kidney	0.00 RPM	100.14 RPM
SRP007412_liver	0.00 RPM	57.87 RPM
SRP007412_testis	0.00 RPM	51.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2227 was not detected

EST

No EST(s) were mapped for retro_mmus_2227 retrocopy.

TSS

No TSS is located nearby retro_mmus_2227 retrocopy 5' end.

Lab

retro_mmus_2227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2227 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1517

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227 ,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,