RetrogeneDB ID: retro_mmus_2908

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:27046891..27047704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Api5
• Ensembl ID: ENSMUSG00000027193
• Aliases: Api5, AAC-11, AI196452
• Description: apoptosis inhibitor 5 [Source:MGI Symbol;Acc:MGI:1888993]

Sequence

>retro_mmus_2908
ATACCGATGGTGGAGGAGCTGTAACACAACTACAGCATCCTCGCCTAAGCCGCAGAGCAAGTGGGCCAGCATAAAGATGC
CTACCAAGTGATACTGGGTGGTGTGAAAGGCAGCACCAAGGAAAAGCAATTAGCAGTTCAGTTTATACCAAAATTGTTCA
AGCATTTTCCAGAGCTGGCTGATTCTGCTACCAATGCAAAGTTAGACCTATGTAAGCATGAGGATGTGCCAATACGACAC
CAAACAATTAAAGAGCTGCCTCAGTTTGCCACAGGAGAAAACTTTCCGAGAGAAGCAGATATACTGACCCAGCTTCTGCA
GATAGATGACTCTGCAGAATTTAATTTGGTGAACAACGCTCTGTTAAGTATATTTGAGATGGATGCAAAAGAAATGTTAG
GTGGCTTGTTTAGCCAGATTCTTCCATGAGAAGACAGTGTTAGAAAATGAGCAATTAAATTCCTGTGCACAAAACTCAAG
ATGCTCCTAGATGAAGTGTTAACTAAGGAAGGAGAGGAGATCACTCTCACTGAATCCAAAATGGTCCAGGAAGATGTGAC
TGGTGAAGTGTTTGTTCTGTTCATGAACATACTGTCTGGTTTAAAAAGCTTACAGGCAGTGAGTGGAAGACAGCAGCTGG
TAGAACAGGCAGCAGACCAGACAGCAGAGCAGGCTGACCTGGAGCAGACCTTCAACCCCTCAGAGCCTGACTGTGTGGAT
AGGCTACTGCAGTGCACGTGGCAGGCAGTGTCTCTGTTCTCTAAACATGTCCATTCTACAAGGTGTGTGACATATTTCTG
TGAGCAGGTTCTT

Alignment

ORF - retro_mmus_2908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.7 %
• Parental protein coverage: 52.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDL
          .P.VEEL..NY.ILA.A.EQVGQHKDAYQVIL.GVKG.TKEK.LA.QFIPK.FKHFPELADSA.NA.LDL
Retrocopy IPMVEEL*HNYSILA*AAEQVGQHKDAYQVILGGVKGSTKEKQLAVQFIPKLFKHFPELADSATNAKLDL

Parental  CEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQI
          C..EDV.IR.Q.IKELPQFATGEN.PR.ADILTQLLQ.DDSAEFNLVNNALLSIF.MDAK..LGGLFSQI
Retrocopy CKHEDVPIRHQTIKELPQFATGENFPREADILTQLLQIDDSAEFNLVNNALLSIFEMDAKEMLGGLFSQI

Parental  LQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFMKILSGLKSLQTVSGR
          L..ED.VR..AIKFL.TKLK.L.DEVLTKE.EE..LTESK.V.EDVTGE.FVLFM.ILSGLKSLQ.VSGR
Retrocopy LP*EDSVRK*AIKFLCTKLKMLLDEVLTKEGEEITLTESKMVQEDVTGEVFVLFMNILSGLKSLQAVSGR

Parental  QQLVELVAEQ----ADLEQAFSPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVL
          QQLVE..A.Q....ADLEQ.F.PS.PDCVDRLLQCT.QAV.LFSK.VHSTR.VTYFCEQVL
Retrocopy QQLVEQAADQTAEQADLEQTFNPSEPDCVDRLLQCTWQAVSLFSKHVHSTRCVTYFCEQVL

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	67.29 RPM
SRP007412_cerebellum	0.00 RPM	75.42 RPM
SRP007412_heart	0.00 RPM	35.05 RPM
SRP007412_kidney	0.00 RPM	58.73 RPM
SRP007412_liver	0.00 RPM	52.73 RPM
SRP007412_testis	0.09 RPM	54.57 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2908 was not detected

EST

No EST(s) were mapped for retro_mmus_2908 retrocopy.

TSS

No TSS is located nearby retro_mmus_2908 retrocopy 5' end.

Lab

retro_mmus_2908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2908 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011993	1 retrocopy	retro_cpor_861,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Macaca mulatta	ENSMMUG00000008827	1 retrocopy	retro_mmul_947,
Mus musculus	ENSMUSG00000027193	1 retrocopy	retro_mmus_2908 ,
Pongo abelii	ENSPPYG00000003345	1 retrocopy	retro_pabe_3805,
Vicugna pacos	ENSVPAG00000012428	1 retrocopy	retro_vpac_289,