RetrogeneDB ID: retro_mmus_3387

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:123867807..123868554(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atg4b
• Ensembl ID: ENSMUSG00000026280
• Aliases: Atg4b, 2510009N07Rik, AW048066, Apg4b, Atg4bl, Autl1
• Description: autophagy related 4B, cysteine peptidase [Source:MGI Symbol;Acc:MGI:1913865]

Sequence

>retro_mmus_3387
GGGCTGAACACTGTTGCCCAGGTCCTCAAGACACTTGCTATATTCGACACATGGGGTTCCTTGGCTGTTCACATGGCAGT
GGACAACACTGTGGTGATGGAGGAAATCAGAAGGTTATTCAGGGCCAGCCTTCCCTATGCTGGGACTGCTGTACTTCATA
CTGATTCAAAGAGGTACTGAAATGGGTTCCCTACTAGACCTGAAGTCATAAACGGGTCATTGGCTTGGAGACCACTAGTG
CTTCTCATCCCTCTCTGCGTGGGACTGACAGACATCAATGAGGCCTATGTGGAGACACTGAAGCACTGTTTCATGATGTC
CCAGTCCCTGGGTGTTATTGGAAGGAAGCCCAACAGTGCCCACTACTTTATTGGCTACATTGGTGAGGAACTCATCTGTC
TGGGCCCCCATGCTACACAGCCTGCAGTGGAGCTGACTGACAGCTGCTTTAACCCTGAGAGCTTCCACTGCCAATACACT
CCCTTTAGGATGGACCTTGGAGAGCTTGACCCATCCATTGTCATGGAATTTTTCTGTAAGACTGAGGAAGACTTTAACGA
CTGGTGTCAGCAAGTCAAAAAGCTATCTCAGCTTTGAGGTGCCCCGTTCATGTTTGAGTTGGTGGAACAGCAGCCTTCTC
ATCTGGCCTGCCAGGATGTCCTGAACCTGTCCCTAGACTCTTCTGATGTAGAGAGACCGGAGAGGTTCTTTGACTCTGAG
GATGAAGACTTTTAAATCTTATCCCTC

Alignment

ORF - retro_mmus_3387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.6 %
• Parental protein coverage: 63.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVMEEIRRLCRANLPCVGAAALPTDSERHCNGFPAGAEVT
          G.NTVAQVLK.LA.FDTW.SLAVH.A.DNTVVMEEIRRL.RA.LP..G.A.L.TDS.R..NGFP...EV.
Retrocopy GLNTVAQVLKTLAIFDTWGSLAVHMAVDNTVVMEEIRRLFRASLPYAGTAVLHTDSKRY*NGFPTRPEVI

Parental  NRPSAWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQ
          N...AWRPLVLLIPL..GLTDINEAYVETLKHCFMM.QSLGVIG.KPNSAHYFIGY.GEELI.L.PH.TQ
Retrocopy NGSLAWRPLVLLIPLCVGLTDINEAYVETLKHCFMMSQSLGVIGRKPNSAHYFIGYIGEELICLGPHATQ

Parental  PAVELTDSCFIPDESFHCQHPPSRMGIGELDPSIAVGFFCKTEEDFNDWCQQVKKLSQLGGALPMFELVE
          PAVELTDSCF.P.ESFHCQ..P.RM..GELDPSI...FFCKTEEDFNDWCQQVKKLSQL.GA..MFELVE
Retrocopy PAVELTDSCFNP-ESFHCQYTPFRMDLGELDPSIVMEFFCKTEEDFNDWCQQVKKLSQL*GAPFMFELVE

Parental  QQPSHLACQDVLNLSLDSSDVERLERFFDSEDEDFEILSL
          QQPSHLACQDVLNLSLDSSDVER.ERFFDSEDEDF.ILSL
Retrocopy QQPSHLACQDVLNLSLDSSDVERPERFFDSEDEDF*ILSL

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	51.59 RPM
SRP007412_cerebellum	0.00 RPM	52.28 RPM
SRP007412_heart	0.00 RPM	22.82 RPM
SRP007412_kidney	0.02 RPM	28.32 RPM
SRP007412_liver	0.00 RPM	21.90 RPM
SRP007412_testis	0.00 RPM	25.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3387 was not detected

EST

No EST(s) were mapped for retro_mmus_3387 retrocopy.

TSS

No TSS is located nearby retro_mmus_3387 retrocopy 5' end.

Lab

retro_mmus_3387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3387 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	ENSMUSG00000026280	1 retrocopy	retro_mmus_3387 ,
Mus musculus	ENSMUSG00000079418	1 retrocopy	retro_mmus_2283,