RetrogeneDB ID: retro_mmus_2717

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:12857396..12858393(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083620
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hormad1
• Ensembl ID: ENSMUSG00000028109
• Aliases: Hormad1, 4921522K05Rik, Nohma
• Description: HORMA domain containing 1 [Source:MGI Symbol;Acc:MGI:1915231]

Sequence

>retro_mmus_2717
GATCTCTGTGTCAAAATTCTGAAAGAAGATAAAAATTGTCCAGGTTCTTCACAGCTAGTGAAGTGGATGCTAGGATGCTA
GGATGCTTTACAGAAGAAATATCTAAGGATGATCATTCTAGCTGTATACACCAATCCAGGAGATCCTCAGACAATTTCAG
GATATTACCAGTTTAAATTCAAGTACACCAAAAATGGACCAATCATGGACTTTATAAGCAAAAATCAAAACAATAAATCT
AGTACAACATCTGCTGACAGCAAGAAAGCAAGCATTCCCCTCATTCGGAAGATTTATGTCTTAATGCAAAATCTAGGACC
ATTACCTAAAGCTGTTTGTCTGACCAGGAAACTTTTTTACTATGATGAAGTTACACCCCCAAATTACCAACCACCAGGTT
TTAAGGATGGTGACTGTGAAGGAGTAATATTTGATGGGAACCCTACATACTTAAATGTGGGAGAAGTCCCAACACCTTTT
CACACCCTCAGATTAAAAGTGACCACTGAGAAGGAACGAATGGAAAATATTGATTCAACCATACTAAAACCAAAAGAATC
AAGAACACAATTTGAAAAAATTCTAAGGGACAAAGATGATGTAGAAGATGAAAAATCATAATAATTTTGACATTAAAACT
AAAATGAACGAACAGAATGAAAACTCTGGAGCTTCTGAAATCAAAGAACCAAATTTAGATTGTAAGGAAGAAGAAACTAT
GCAATTCAAAAAGAGCCAAAGTCCTTCAATTTCTCATTGTCAGGTTGAACAGTTAGTCAGTAAAACATCTGAACTTGATG
TGTCTGAAAGCAAAACAAGAAGCGGAAAAATCTTTCAGAGTAAAATGGTAAATGGAAATAATCAACAAGGACAAACGTCT
AAAGAAAATTGGAAGAGAGGTCTTCGTCAATTTGGGAAAACAGTCCTTCACGTCTTGGAATCTAGTCAAGAGTCAGTGCT
GAAGAAAAGGAGAGTTAGTGAACCAAAGGAACATACC

Alignment

ORF - retro_mmus_2717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.79 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLCVKILKEDKNCPGSSQLVKWMLGCYDALQKKYLRMIILAVYTNPGDPQTISECYQFKFKYTKNGPIMD
          DLCVKILKEDKNCPGSSQLVK........LQKKYLRMIILAVYTNPGDPQTIS..YQFKFKYTKNGPIMD
Retrocopy DLCVKILKEDKNCPGSSQLVKXXXXXXXXLQKKYLRMIILAVYTNPGDPQTISGYYQFKFKYTKNGPIMD

Parental  FISKNQNNKSSTTSADTKKASILLIRKIYVLMQNLGPLPNDVCLTMKLFYYDEVTPPDYQPPGFKDGDCE
          FISKNQNNKSSTTSAD.KKASI.LIRKIYVLMQNLGPLP..VCLT.KLFYYDEVTPP.YQPPGFKDGDCE
Retrocopy FISKNQNNKSSTTSADSKKASIPLIRKIYVLMQNLGPLPKAVCLTRKLFYYDEVTPPNYQPPGFKDGDCE

Parental  GVIFDGDPTYLNVGEVPTPFHTFRLKVTTEKERMENIDSTILKPKESKTQFEKILMDKDDVEDE-NHNNF
          GVIFDG.PTYLNVGEVPTPFHT.RLKVTTEKERMENIDSTILKPKES.TQFEKIL.DKDDVEDE.NHNNF
Retrocopy GVIFDGNPTYLNVGEVPTPFHTLRLKVTTEKERMENIDSTILKPKESRTQFEKILRDKDDVEDE>NHNNF

Parental  DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ
          DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ
Retrocopy DIKTKMNEQNENSGASEIKEPNLDCKEEETMQFKKSQSPSISHCQVEQLVSKTSELDVSESKTRSGKIFQ

Parental  SKMVNGNNQQGQTSKENRKRSLRQFRKTVLHVLESSQESVLKKRRVSEPKEHT
          SKMVNGNNQQGQTSKEN.KR.LRQF.KTVLHVLESSQESVLKKRRVSEPKEHT
Retrocopy SKMVNGNNQQGQTSKENWKRGLRQFGKTVLHVLESSQESVLKKRRVSEPKEHT

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.32 RPM	30.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2717 was not detected

EST

No EST(s) were mapped for retro_mmus_2717 retrocopy.

TSS

No TSS is located nearby retro_mmus_2717 retrocopy 5' end.

Lab

retro_mmus_2717 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2717 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000071	1 retrocopy	retro_dnov_2620,
Homo sapiens	ENSG00000143452	1 retrocopy	retro_hsap_3612,
Mus musculus	ENSMUSG00000028109	2 retrocopies	retro_mmus_1420, retro_mmus_2717 ,
Otolemur garnettii	ENSOGAG00000005640	1 retrocopy	retro_ogar_1908,
Rattus norvegicus	ENSRNOG00000021160	1 retrocopy	retro_rnor_1772,
Tarsius syrichta	ENSTSYG00000006025	1 retrocopy	retro_tsyr_1426,