RetrogeneDB ID: retro_mmus_3017

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:39445832..39446174(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046372
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam32a
• Ensembl ID: ENSMUSG00000003039
• Aliases: Fam32a, 2510049I19Rik, AW822030, OTAG-12, Otag12
• Description: family with sequence similarity 32, member A [Source:MGI Symbol;Acc:MGI:1915172]

Sequence

>retro_mmus_3017
ATGGAGGCTTATGAGCAGGTTCAGAAGGGCCCCCTAAAGCTGAAAGGCGTGGCGGAGCTTGGTGTGACAAAGCGAAAGAA
GAAGAAGGACAAAGACAAGGACAAGGCCAAGATTCTGGAGGCCATGGGGACGAGCAAGAAGAGTGAGGAGGAGGAGAAGA
GGCGCTGCCTGGACAAGCGCACACCGGCGCAGGCAGCCTTCGAAAAGATGCAGGAGAAGCGGCAAATGGAAAGAATCTTG
AAGAAGGCGTCAAAAACCCACAAGCAGAGAGTGGAGGACTTCAACCGACACCTGGATACACTCACTGAGCACTATGACAT
CCCCAAAGTCAGCTGGACCAAG

Alignment

ORF - retro_mmus_3017 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAYEQVQKGPLKLKGVAELGVTKRK-KKKKDKDKAKMLEAMGTSKKS-EEEKRRCLDKRTPAQAAFEKM
          MEAYEQVQKGPLKLKGVAELGVTKRK.K..........LEAMGTSKKS.EEEKRRCLDKRTPAQAAFEKM
Retrocopy MEAYEQVQKGPLKLKGVAELGVTKRKKKXXXXXXXXXILEAMGTSKKSEEEEKRRCLDKRTPAQAAFEKM

Parental  QEKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK
          QEKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK
Retrocopy QEKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK

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	0.07 RPM	62.19 RPM
SRP007412_cerebellum	0.13 RPM	73.16 RPM
SRP007412_heart	0.00 RPM	28.14 RPM
SRP007412_kidney	0.00 RPM	70.05 RPM
SRP007412_liver	0.08 RPM	52.76 RPM
SRP007412_testis	0.23 RPM	25.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3017 was not detected

EST

No EST(s) were mapped for retro_mmus_3017 retrocopy.

TSS

No TSS is located nearby retro_mmus_3017 retrocopy 5' end.

Lab

retro_mmus_3017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3017 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Homo sapiens	ENSG00000105058	4 retrocopies	retro_hsap_1116, retro_hsap_1950, retro_hsap_2541, retro_hsap_693,
Gorilla gorilla	ENSGGOG00000022418	4 retrocopies	retro_ggor_1420, retro_ggor_1587, retro_ggor_592, retro_ggor_872,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654,
Microcebus murinus	ENSMICG00000013721	3 retrocopies	retro_mmur_1449, retro_mmur_252, retro_mmur_500,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mustela putorius furo	ENSMPUG00000016048	1 retrocopy	retro_mputfur_1493,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017 ,
Nomascus leucogenys	ENSNLEG00000005441	3 retrocopies	retro_nleu_192, retro_nleu_2227, retro_nleu_2790,
Oryctolagus cuniculus	ENSOCUG00000002238	1 retrocopy	retro_ocun_1275,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Pan troglodytes	ENSPTRG00000010641	4 retrocopies	retro_ptro_1304, retro_ptro_1480, retro_ptro_497, retro_ptro_684,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,
Sus scrofa	ENSSSCG00000013855	2 retrocopies	retro_sscr_292, retro_sscr_870,
Tarsius syrichta	ENSTSYG00000009106	1 retrocopy	retro_tsyr_418,