RetrogeneDB ID: retro_mmus_2093

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:134762826..134763630(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083879
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zfand1
• Ensembl ID: ENSMUSG00000039795
• Aliases: Zfand1, 2310008M20Rik, AW048890
• Description: zinc finger, AN1-type domain 1 [Source:MGI Symbol;Acc:MGI:1913611]

Sequence

>retro_mmus_2093
ATGGCGGAGTTGGACATTGGGCAGCACTGCCAGGTGCAGCACTGCCGGCAGCGAGATTTTCTTCCATTTGTGTGTGATGG
TTGTTCAGGAATATTTTGCCTTGAACACAGAAGCAAGGACTCTCATGGTTGTTCTGAGGTGAATGTAGTCAAGGAGAGAC
CAAAGACAGATGAACACAAATCTTACTCATGCTCTTTCAAGGGCTGCACTGACGTAGAGCTTGTGGCAGTGATCTGTCCT
TACTGTGAGAAGAACTTTTGCCTGAGACACCGTCATCAGTCGGATCATGACTGTGAAAAGCTGGAAGTCGCAAAGCCTCG
AATGGCTGCCACACAGAAACTTGTCAGAGACATTGTCGATGCCAAGACAGGAGGGGCAGCAAGTAAGGGACGGAAAGGCG
CAAAAAGCAGCGGAACAGCGGCGAAGGTGGCGCTGATGAAGCTAAAGATGCACGCTGATGGGGATAAGTCCCTGCCGCAG
ACAGAAAGAACATACTTCCAGGTGTACTTGCCAAAGGGGAGCAAGGAAAAAAGCAAAGCCATGTTCTTTTGCCTGCGGTG
GAGCATCGGGAAGGTTGTGGACTTTGCAGCTTCTCTCGCTAATCTCAGGAATGAAAACAACAAGCTGACGGCGAAGAAGC
TGAGGCTGTGTCACGTCCCTTCAGGAGAAGCCCTGCCATTGGATCACACATTGGAAAGGTGGATCACGAAGGAGGAGTGC
CCTTTATATAATGGAGGAAATGTTATCTTGGAATATCTTAACGATGAAGAGCAGTTTTTAAAAAATGTTGACTCTTACTT
GGAA

Alignment

ORF - retro_mmus_2093 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAELDIGQHCQVQHCRQRDFLPFVCDGCSGIFCLEHRSKDSHGCSEVNVVKERPKTDEHKSYSCSFKGCT
          MAELDIGQHCQVQHCRQRDFLPFVCDGCSGIFCLEHRSKDSHGCSEVNVVKERPKTDEHKSYSCSFKGCT
Retrocopy MAELDIGQHCQVQHCRQRDFLPFVCDGCSGIFCLEHRSKDSHGCSEVNVVKERPKTDEHKSYSCSFKGCT

Parental  DVELVAVICPYCEKNFCLRHRHQSDHDCEKLEVAKPRMAATQKLVRDIVDAKTGGAASKGRKGAKSSGTA
          DVELVAVICPYCEKNFCLRHRHQSDHDCEKLEVAKPRMAATQKLVRDIVDAKTGGAASKGRKGAKSSGTA
Retrocopy DVELVAVICPYCEKNFCLRHRHQSDHDCEKLEVAKPRMAATQKLVRDIVDAKTGGAASKGRKGAKSSGTA

Parental  AKVALMKLKMHADGDKSLPQTERTYFQVYLPKGSKEKSKAMFFCLRWSIGKVVDFAASLANLRNENNKLT
          AKVALMKLKMHADGDKSLPQTERTYFQVYLPKGSKEKSKAMFFCLRWSIGKVVDFAASLANLRNENNKLT
Retrocopy AKVALMKLKMHADGDKSLPQTERTYFQVYLPKGSKEKSKAMFFCLRWSIGKVVDFAASLANLRNENNKLT

Parental  AKKLRLCHVPSGEALPLDHTLERWITKEECPLYNGGNVILEYLNDEEQFLKNVDSYLE
          AKKLRLCHVPSGEALPLDHTLERWITKEECPLYNGGNVILEYLNDEEQFLKNVDSYLE
Retrocopy AKKLRLCHVPSGEALPLDHTLERWITKEECPLYNGGNVILEYLNDEEQFLKNVDSYLE

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	10.23 RPM
SRP007412_cerebellum	0.00 RPM	6.17 RPM
SRP007412_heart	0.03 RPM	11.55 RPM
SRP007412_kidney	0.12 RPM	13.21 RPM
SRP007412_liver	0.05 RPM	8.41 RPM
SRP007412_testis	0.05 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2093 was not detected

EST

No EST(s) were mapped for retro_mmus_2093 retrocopy.

TSS

No TSS is located nearby retro_mmus_2093 retrocopy 5' end.

Lab

retro_mmus_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014075	1 retrocopy	retro_cpor_312,
Homo sapiens	ENSG00000104231	1 retrocopy	retro_hsap_187,
Gorilla gorilla	ENSGGOG00000023665	1 retrocopy	retro_ggor_268,
Microcebus murinus	ENSMICG00000016889	1 retrocopy	retro_mmur_1073,
Macaca mulatta	ENSMMUG00000002626	1 retrocopy	retro_mmul_394,
Mus musculus	ENSMUSG00000039795	1 retrocopy	retro_mmus_2093 ,
Nomascus leucogenys	ENSNLEG00000002584	1 retrocopy	retro_nleu_997,
Otolemur garnettii	ENSOGAG00000009813	2 retrocopies	retro_ogar_2608, retro_ogar_514,
Tupaia belangeri	ENSTBEG00000015393	1 retrocopy	retro_tbel_3648,