RetrogeneDB ID: retro_mmus_1566

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:35400798..35401761(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092560
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Arcn1
• Ensembl ID: ENSMUSG00000032096
• Aliases: Arcn1, 4632432M07Rik, nur17
• Description: archain 1 [Source:MGI Symbol;Acc:MGI:2387591]

Sequence

>retro_mmus_1566
ATGGTGCTGTTGGCAGCAGCAGTCTGCACGAATGCGAGAAAGGCTATTGTTTCTCGACAGTTCGTGGAGATGACCCGAAC
TCGGATTGAAGGCTTATTAGCAGCTTTCCCAAAACTCATGAACACTGGAAAACAGCATACTTTTGTTGAAACAGAGAGTG
TAAGATATGTGTACCAACCTATGGAGAAACTGTACATGGTATTGATCACTACAAAGAACAGCAATATCTTAGAAGCTTTG
GAGACTTTAAGGCTCTTCTCAAGGGTGATCCCTGAATATTGCCGAGCCTCAGAGGAAAATGAAATATCTGAGCACTGTTT
TGATTTGATTTTTGCTTTTGATGAAATTGTTGCCATGGGATGCCGGGAGAATGTTAACCTGGCACAGATCAGAACCTTCA
CAGAAATGGACTCTCACGAGGAGAAAGTATTCTGAGCAGTCAGAGAGACTCAAGAACGTGGAGCTAAGGCTGAGACGCGG
CGTAAAGCAAAGGAATTACAACAGGCCCGAAGAGATGCAGAGAGACAGGGGAAAAAAACACCAGAATTTGGCGGATTTGG
TAGTTCTGCAGTGTCTGGAGGCAGCACAGCAGCCATGATCACAGAGACTATCATTGAAACTGATAAACCAAAAGTGGCGC
CTGCACCAGCCAGACCTTCAGGCCCCAGCAAGGCTTTGAAACTTGGAGCTAAAGGGAAGGAAGTAGATAACTTTGTGGAC
AAATTGAAATCTGAAGGTGAAACTATTATGTCTTCTAATATGGGAAAACGTACCTCAGAAGCAACCAGAGTGCATGTTCC
ACCTATTAATATGTAAAGTATGCACATGAAGATTGAAGAGAAGATCACACTAACCTGTGGGAGAGATGGAGGATTACAGA
ATATGGAGTTGCATGGCATGATCATGCTTAGGATCTCAGGTGACAAATTTGGCCGGATTTGTCTTCATGTAGAAAAAGAA
GAT

Alignment

ORF - retro_mmus_1566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 62.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETESVRYVYQPMEKLYMVLIT
          MVLLAAAVCT.A.KAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETESVRYVYQPMEKLYMVLIT
Retrocopy MVLLAAAVCTNARKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETESVRYVYQPMEKLYMVLIT

Parental  TKNSNILEDLETLRLFSRVIPEYCRALEENEISEHCFDLIFAFDEIVALGYRENVNLAQIRTFTEMDSHE
          TKNSNILE.LETLRLFSRVIPEYCRA.EENEISEHCFDLIFAFDEIVA.G.RENVNLAQIRTFTEMDSHE
Retrocopy TKNSNILEALETLRLFSRVIPEYCRASEENEISEHCFDLIFAFDEIVAMGCRENVNLAQIRTFTEMDSHE

Parental  EKVFRAVRETQEREAKAEMRRKAKELQQARRDAERQGKKAPGFGGFGSSAVSGGSTAAMITETIIETDKP
          EKVF.AVRETQER.AKAE.RRKAKELQQARRDAERQGKK.P.FGGFGSSAVSGGSTAAMITETIIETDKP
Retrocopy EKVF*AVRETQERGAKAETRRKAKELQQARRDAERQGKKTPEFGGFGSSAVSGGSTAAMITETIIETDKP

Parental  KVAPAPARPSGPSKALKLGAKGKEVDNFVDKLKSEGETIMSSNMGKRTSEATKVHAPPINMESVHMKIEE
          KVAPAPARPSGPSKALKLGAKGKEVDNFVDKLKSEGETIMSSNMGKRTSEAT.VH.PPINM.S.HMKIEE
Retrocopy KVAPAPARPSGPSKALKLGAKGKEVDNFVDKLKSEGETIMSSNMGKRTSEATRVHVPPINM*SMHMKIEE

Parental  KITLTCGRDGGLQNMELHGMIMLRISDDKFGRIRLHVENED
          KITLTCGRDGGLQNMELHGMIMLRIS.DKFGRI.LHVE.ED
Retrocopy KITLTCGRDGGLQNMELHGMIMLRISGDKFGRICLHVEKED

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	87.49 RPM
SRP007412_cerebellum	0.00 RPM	84.41 RPM
SRP007412_heart	0.00 RPM	73.41 RPM
SRP007412_kidney	0.00 RPM	127.57 RPM
SRP007412_liver	0.00 RPM	118.27 RPM
SRP007412_testis	0.00 RPM	52.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1566 was not detected

EST

No EST(s) were mapped for retro_mmus_1566 retrocopy.

TSS

No TSS is located nearby retro_mmus_1566 retrocopy 5' end.

Lab

retro_mmus_1566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000032096	2 retrocopies	retro_mmus_1566 , retro_mmus_1567,