RetrogeneDB ID: retro_mmus_3020

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:41326129..41326950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Xiap
• Ensembl ID: ENSMUSG00000025860
• Aliases: Xiap, 1110015C02Rik, Aipa, Api3, Birc4, IAP3, ILP-1, MIHA, mXIAP
• Description: X-linked inhibitor of apoptosis [Source:MGI Symbol;Acc:MGI:107572]

Sequence

>retro_mmus_3020
GTCAGAAACAGAAAACATTTTGCTCTTGACAGGCCATCTGAGACTCAGCAGATTATCTCTTGAGAACTGGACAGGCTGTA
GATATTTCAGACACGATATACCCAAGGAACCCTGGCATGTGTAGTGAAGAAGCTAGACTGAAGTCATTTCAGAACTGGAC
GGACTATGCTCATTTAACCCACAGGTAGTTAGCTAGTGCTGGCCTCTATTACACAGGGGCTGATGATCAAGTGCAATGCT
TTTGTTGTGGTGGAAAACTGAAAAATCGGGAACCCTGTGATCGTGCCTGGTCAGAACACAGGAGATTCTTTACCAATTGC
TTCTTTGTTTTGGGCCAGCACATTAATGTTCGAAGTGAATCTGGTGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAA
TTCTCCAAGAAATCCAGCCATGGCAGAATATGAAGCACGGGTCGTTACTTTTGGAACATGGATATACTCAGTTAACAAGG
AGCAGCTTGCAAGAGCTGGATTTTATGCTTTAGGTGAAGGCGATAAAGTGAAGTGCTTTCACTGTGGAGGAGGGCTCACG
GTTTGGAAGCCAAGTGAAGAATCCTGGGACCAGCATGCTAAGTGCTATCCAGGGTGTAAATATCTATTGGATGAGAAGGG
GCAAGAATATATAAATAATATTCATTTAACCCATTCACTTGAGGAATCTTTGGGAAGAACTCCTGAAAAAACACCACCAC
TAACTTAAAAAAAAATCAATGATATCATCTTTCAAAATCCTATGGTGCAAGAAGCTATACAAATGAGATTTAGCTTCAAG
GACATTAAGAAAACAGTGGAA

Alignment

ORF - retro_mmus_3020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 55.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGNRNPFAPDRPPETH-ADYLLRTGQVVDISDTIYPRNPAMCSEEARLKSFQNWPDYAHLTPRELASAGL
          V.NR..FA.DRP.ET..ADYLLRTGQ.VDISDTIYPRNP.MCSEEARLKSFQNW.DYAHLT.R.LASAGL
Retrocopy VRNRKHFALDRPSETQ<ADYLLRTGQAVDISDTIYPRNPGMCSEEARLKSFQNWTDYAHLTHR*LASAGL

Parental  YYTGADDQVQCFCCGGKLKNWEPCDRAWSEHRRHFPNCFFVLGRNVNVRSESGVSSDRNFPNSTNSPRNP
          YYTGADDQVQCFCCGGKLKN.EPCDRAWSEHRR.F.NCFFVLG...NVRSESGVSSDRNFPNSTNSPRNP
Retrocopy YYTGADDQVQCFCCGGKLKNREPCDRAWSEHRRFFTNCFFVLGQHINVRSESGVSSDRNFPNSTNSPRNP

Parental  AMAEYEARIVTFGTWTSSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYL
          AMAEYEAR.VTFGTW..SVNKEQLARAGFYALGEGDKVKCFHCGGGLT.WKPSE..W.QHAK.YPGCKYL
Retrocopy AMAEYEARVVTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTVWKPSEESWDQHAKCYPGCKYL

Parental  LDEKGQEYINNIHLTHSLEESLGRTAEKTPSLT-KKIDDTIFQNPMVQEAIRMGFSFKDIKKTME
          LDEKGQEYINNIHLTHSLEESLGRT.EKTP.LT.....D.IFQNPMVQEAI.M.FSFKDIKKT.E
Retrocopy LDEKGQEYINNIHLTHSLEESLGRTPEKTPPLTXXXXNDIIFQNPMVQEAIQMRFSFKDIKKTVE

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	91.47 RPM
SRP007412_cerebellum	0.00 RPM	91.18 RPM
SRP007412_heart	0.00 RPM	39.35 RPM
SRP007412_kidney	0.02 RPM	64.66 RPM
SRP007412_liver	0.03 RPM	104.54 RPM
SRP007412_testis	0.00 RPM	5.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3020 was not detected

EST

No EST(s) were mapped for retro_mmus_3020 retrocopy.

TSS

No TSS is located nearby retro_mmus_3020 retrocopy 5' end.

Lab

retro_mmus_3020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3020 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025860	1 retrocopy	retro_mmus_3020 ,
Oryctolagus cuniculus	ENSOCUG00000009878	1 retrocopy	retro_ocun_82,