RetrogeneDB ID: retro_mmus_2292

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:114544379..114544766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam162b
• Ensembl ID: ENSMUSG00000019909
• Aliases: Fam162b, 9430073N08Rik
• Description: family with sequence similarity 162, member B [Source:MGI Symbol;Acc:MGI:1924546]

Sequence

>retro_mmus_2292
CAGTGGCCTGAATGAGGTCTCTAGATAGCAGGCCACCTGAGGAGCTTTAATGGTTAGAATGCCAATGGCTTTGTGCCCCT
GGAGAAAGTTCACAGGATCCCTGCCTAGTGCAAGTCTTCACAATTCCACTAGAATATCCTGCTGTGAATCAGTCACTTTA
AATCCACAGAGAAGATTCTGCTTCTGGCACTGTCTGAGAAGATAGCTGCAGGGAAAACAAAGCTCAAGGGAAAGGTTGTT
ACATAATCATCAGGCACACATCATTGCCTGCTTTGCTGTGATTGTGTCTGCCAAGAGGGCTATAGAGCAACATGAATCCT
TAACACGTAGGATTCTGGCAAAGCAAACTAGGTGACATGAAAAAGCATATTGGCTGCAGAGTCTAAG

Alignment

ORF - retro_mmus_2292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 82.8 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RWPRWGPRVACHPCSSSGQNPSGFEPPEKVHRIPAQYKPSKFDKKILLWTGRFKSIEDIPPLVPPEMIAV
          .WP..G...A.H..S..G.N..GF.P.EKVHRIPA..K.S.F...ILL....FKS.E.I..L...E.IA.
Retrocopy QWPE*GL*IAGHLRSFNG*NANGFVPLEKVHRIPA*CKSSQFH*NILL*ISHFKSTEKILLLALSEKIAA

Parental  SR-NKARVKACYIMIGLT-IVACFAVIVSAKRAVERHESLTSWNLAKKAKWREEA-ALAAQSK
          ...NKA..K.CYI.I..T.I.ACFAVIVSAKRA.E.HESLT...LAK.....E.A..LAA.SK
Retrocopy GK<NKAQGKGCYIIIRHT<IIACFAVIVSAKRAIEQHESLTRRILAKQTR*HEKA<ILAAESK

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	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2292 was not detected

EST

No EST(s) were mapped for retro_mmus_2292 retrocopy.

TSS

No TSS is located nearby retro_mmus_2292 retrocopy 5' end.

Lab

retro_mmus_2292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2292 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183807	2 retrocopies	retro_hsap_3744, retro_hsap_901,
Gorilla gorilla	ENSGGOG00000002045	1 retrocopy	retro_ggor_728,
Microcebus murinus	ENSMICG00000014555	1 retrocopy	retro_mmur_746,
Mus musculus	ENSMUSG00000019909	1 retrocopy	retro_mmus_2292 ,
Pan troglodytes	ENSPTRG00000018538	4 retrocopies	retro_ptro_2541, retro_ptro_2542, retro_ptro_2994, retro_ptro_621,