RetrogeneDB ID: retro_mmus_857

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:44222240..44223197(+)
• Located in intron of: ENSMUSG00000036257

Retrocopy information

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

Parental gene information

• Parental gene symbol: Naf1
• Ensembl ID: ENSMUSG00000014907
• Aliases: Naf1, Gm174
• Description: nuclear assembly factor 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2682306]

Sequence

>retro_mmus_857
CCAGTGCTGCAGGCCTCGGACTCCTTGGACTCGGATTCGGACAGTGAAACAGATTCAGATAGCTCAAGCTCCTCCTCTTC
GTCGTCCTCTTCATCTTCATCCTGTGTATCATTTCCTCCTGTGATGTCAGATGGACATGAGGATGTCCAAGTTGAAAAAG
AAAATAAGAATTTTCCTCTTAAAACAAGAGATGAATTGCTTCTTAATGAACTACCTTCTGTTGAAGAACTCACTATAATT
CTGCCTGAAGACATTGCACTAAAGCCTCTTGGGAAAGTTTCAAGCATTATTGAGCAATTAGTAATAATTGAGTCTGTGAC
TAACATACCTCCAGTTAATGAAGATACTGTCATTTTCAAAAGTGATCGACAAGCAGCAGGGAAGATATTTGAGATATTTG
GACCTGTTGCCCATCCATTTTATGTGTTACGGTTTAATTCATCAGATCACATTGAGAGTAAAGGTATCAAAATAAATGAC
ACTATGTATTTTGCCCCATCAATGAAAGACTTCACTCAATATATATTCACAGAAAAGCTCAAACAGGACAGAGGATCGGA
CGCTTCTTGGGAGAATGATCAGGAACCCCCTCCAGAAGTCTTGGACTTCAGTGACGATGAGAAAGAAAAAGAAGCCAAAC
AGAGAAAAAAATCTCAGATTCAAGGCCGCAAAAACCTCAAATCTGAATTGAATGAGCCATGTGAAGATTTTGGTGAAGTG
ATTCAGAAGTGGAATGCTTATAGCTCTTCAAAAGGATCTCACCACAGGGAATTCTCAAGAGGCTTTGCGAGGGGTAGATA
CTCTCGAAGAAGCCATGGCAGGCCTCCACCTCAGCAGTGCTATAACTCAGATCATATGACATCTCAAGAGAGTTTGGGAT
TTGCACCTCAGAGACAAGATAATCCTGTCATGCCCCACTATCCTTTTCCCCCGCCCATGTTTGATATGCATATCTTT

Alignment

ORF - retro_mmus_857 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.17 %
• Parental protein coverage: 53.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVLQASDSSDSDSDSETDSDSSSSSSSSSSSSSSCVSFPPVLSDGDEDFQLEKENKNFPLKTKDELLLNE
          PVLQASDS.DSDSDSETDSDSSSSSSSSSSSSSSCVSFPPV.SDG.ED.Q.EKENKNFPLKT.DELLLNE
Retrocopy PVLQASDSLDSDSDSETDSDSSSSSSSSSSSSSSCVSFPPVMSDGHEDVQVEKENKNFPLKTRDELLLNE

Parental  LPSVEELTVILPEDIALKPLGKVSSIIEQLVIIESVTNIPPVNEDTVIFKSDRQAAGKIFEIFGPVAHPF
          LPSVEELT.ILPEDIALKPLGKVSSIIEQLVIIESVTNIPPVNEDTVIFKSDRQAAGKIFEIFGPVAHPF
Retrocopy LPSVEELTIILPEDIALKPLGKVSSIIEQLVIIESVTNIPPVNEDTVIFKSDRQAAGKIFEIFGPVAHPF

Parental  YVLRFNSSDHIESKGIKINDTMYFAPSMKDFTQYIFTEKLKQDRGSDASWKNDQEPPPEVLDFSDDEKEK
          YVLRFNSSDHIESKGIKINDTMYFAPSMKDFTQYIFTEKLKQDRGSDASW.NDQEPPPEVLDFSDDEKEK
Retrocopy YVLRFNSSDHIESKGIKINDTMYFAPSMKDFTQYIFTEKLKQDRGSDASWENDQEPPPEVLDFSDDEKEK

Parental  EAKQRKKSQIQGRKKLKSELNESGEDFGEVHENWNAYSSSEHSKGYHHREFSRGFARGRYSRRSHGRPPP
          EAKQRKKSQIQGRK.LKSELNE..EDFGEV...WNAYSSS...KG.HHREFSRGFARGRYSRRSHGRPPP
Retrocopy EAKQRKKSQIQGRKNLKSELNEPCEDFGEVIQKWNAYSSS---KGSHHREFSRGFARGRYSRRSHGRPPP

Parental  QQYYNSDHMASQESLGFTPQRQDNPVMPHYPFPPPMFDMHNF
          QQ.YNSDHM.SQESLGF.PQRQDNPVMPHYPFPPPMFDMH.F
Retrocopy QQCYNSDHMTSQESLGFAPQRQDNPVMPHYPFPPPMFDMHIF

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	0.14 RPM	10.44 RPM
SRP007412_cerebellum	0.17 RPM	6.30 RPM
SRP007412_heart	0.03 RPM	4.42 RPM
SRP007412_kidney	0.00 RPM	7.83 RPM
SRP007412_liver	0.00 RPM	2.49 RPM
SRP007412_testis	0.23 RPM	13.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_857 was not detected

EST

No EST(s) were mapped for retro_mmus_857 retrocopy.

TSS

No TSS is located nearby retro_mmus_857 retrocopy 5' end.

Lab

retro_mmus_857 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_857 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000014907	1 retrocopy	retro_mmus_857 ,