RetrogeneDB ID: retro_mmus_3472

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:75010592..75011605(+)
• Located in intron of: ENSMUSG00000032750

Retrocopy information

• Ensembl ID: ENSMUSG00000082873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Acbd5
• Ensembl ID: ENSMUSG00000026781
• Aliases: Acbd5, 1300014E15Rik
• Description: acyl-Coenzyme A binding domain containing 5 [Source:MGI Symbol;Acc:MGI:1921409]

Sequence

>retro_mmus_3472
CTTGGTAATGTTCTGACCTCTTCAAATTCCAAAGCTGTTAGTGGTAAAGCGGAGAGCAATGATAGTGGTGCTGAGTCTAA
GGAAGAAGAGGCCCAAGAAGAGTTAAAAGGAGCAGAATAGAGTGGCAGTGATGATAAGAAAATGATGAAATAATCAACAG
ATAAGAATTTGGAAATCATTGTTACCAACGTCTATAAAGGTAGCTTTGCTCAAGATATACAGAGTAATATTCATACTGAT
TCTTCCCGGAGTACCAGAGCAGTGAAGATGAAAAGCCTGGAGATCATAGCTTGCAGCAGACAGGAAACACTGTTGTCTAT
GTTCACCAAGATACAAATGAAGATCCCAGTGAAGATGTTTCAGGAATACATCATTTGACAAGTGATTCCGATAGTGAAGT
ATACTGTGCTTCTATGGAGCAATTTGGACAAGAGTATTACTTAGGTGGTGATCCTACTCAGCACTTGGAAAGTTCTGGGT
TTTGTGAAGATGCTCAACAATCTCCTGGAAATGGCACCATTGGGGAAATGTGGATGGTAGCAGTCAAAGGACAAGGTAAA
ATGTAATAAGAAGGAGAAGATGACAGAAGTAGCAGTGGAGTGCCGCACCATGAGAAAAGAGGTGGAAAGAGCAAGGACTT
CTCCAGTGTCAGGAGAGGGAGAGTAGGGCATAGAATGCCACATTTGAGTGAAGGAACCAAGGGTCAGCAAGTAGGAAGTG
GAGGTAATGGAGAACGCTGGGGCTCAGGATGAGGGTCCAGAAGCAGCCTCAATGAGCATATCACTCTTGTGCTCATTACA
ATGCAGGATGACATGCAGAATGTCCTTCAGAGACTTCATAAACTAGAGACACTAATTGCTTTGCAGGCAAAATTATCTTT
GCAGACAAGTAATCAGCCCTCCTCACAGAGACAATCTTGGTGGCCCTTTGAGATGTTCCCTGGTGCATTAGCTTCTGCTA
TTATATGGCCTTTTATTGTTCACTGGTTGGTGCATTTGTATTATCAAAGAAGG

Alignment

ORF - retro_mmus_3472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 71.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGNVLTSSNAKAVNGKAESSDSGAESEEEEAQEELKGAEQSGSDDKKTLKKSADKNLEIIVTNGYKGSFV
          LGNVLTSSN.KAV.GKAES.DSGAES.EEEAQEELKGAE.SGSDDKK..K.S.DKNLEIIVTN.YKGSF.
Retrocopy LGNVLTSSNSKAVSGKAESNDSGAESKEEEAQEELKGAE*SGSDDKKMMK*STDKNLEIIVTNVYKGSFA

Parental  QDIQSDIHTDSSRSTR-SSEDEKPGDESSQQTGHTIVCAHQDRNEDPSEDASGIHHLTSDSDSEVYCDSM
          QDIQS.IHTDSSRSTR.SSEDEKPGD.S.QQTG.T.V..HQD.NEDPSED.SGIHHLTSDSDSEVYC.SM
Retrocopy QDIQSNIHTDSSRSTR<SSEDEKPGDHSLQQTGNTVVYVHQDTNEDPSEDVSGIHHLTSDSDSEVYCASM

Parental  EQFGQEEYYLGGDPTQHLESSGFCEDAQQSPGNGSIGKMWMVAVKGKGEVKHGGEDGRSSSGAPHRETRG
          EQFGQ.EYYLGGDPTQHLESSGFCEDAQQSPGNG.IG.MWMVAVKG.G.....GED.RSSSG.PH.E.RG
Retrocopy EQFGQ-EYYLGGDPTQHLESSGFCEDAQQSPGNGTIGEMWMVAVKGQGKM**EGEDDRSSSGVPHHEKRG

Parental  GESEDFSSVRRGRVGNRIPHLSEGPKGRQVGSGGDGERWGSDRGSRGSLNEQIALVLIRLQEDMQNVLQR
          G.S.DFSSVRRGRVG.R.PHLSEG.KG.QVGSGG.GERWGS..GSR.SLNE.I.LVLI..Q.DMQNVLQR
Retrocopy GKSKDFSSVRRGRVGHRMPHLSEGTKGQQVGSGGNGERWGSG*GSRSSLNEHITLVLITMQDDMQNVLQR

Parental  LHKLETLTASQAKLSLQTSNQPSSQRPAWWPFEMSPGALAFAIIWPFIAQWLAHLYYQRR
          LHKLETL.A.QAKLSLQTSNQPSSQR..WWPFEM.PGALA.AIIWPFI..WL.HLYYQRR
Retrocopy LHKLETLIALQAKLSLQTSNQPSSQRQSWWPFEMFPGALASAIIWPFIVHWLVHLYYQRR

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	0.09 RPM	57.59 RPM
SRP007412_cerebellum	0.04 RPM	64.00 RPM
SRP007412_heart	0.00 RPM	22.79 RPM
SRP007412_kidney	0.08 RPM	85.49 RPM
SRP007412_liver	0.05 RPM	213.80 RPM
SRP007412_testis	0.00 RPM	41.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3472 was not detected

EST

No EST(s) were mapped for retro_mmus_3472 retrocopy.

TSS

No TSS is located nearby retro_mmus_3472 retrocopy 5' end.

Lab

retro_mmus_3472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000026781	1 retrocopy	retro_mmus_3472 ,