RetrogeneDB ID: retro_mmus_2360

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:70047358..70048174(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082368
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hibadh
• Ensembl ID: ENSMUSG00000029776
• Aliases: Hibadh, 6430402H10Rik, AI265272
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:MGI Symbol;Acc:MGI:1889802]

Sequence

>retro_mmus_2360
CTCATGAAACATGGCTATCCACTCATCCTCTGTGATGTGTTCCCTGGTGTATGCAAAGAGTTTAAAGAGGCTGGGGAACA
GGTAGTGTCCTCCCCATCAGAAGTAGACGGAAAGGCTGACAGCATTATCACAATGCTGCCCTCCAGTATGAATTCAGTAG
AAGTTTATTCTGGAGCAAATAGAATTCTAAAAAAAAAAAAAAAAGTGAAGAACGGTTCATTATTAATAGATTCCAGTACT
ATTGATCCTTCAGTTTCAAAAGAATTGGCAAAAGAAGTTGAGAAAATGGGAGCTGTTTTCATGGACTCCCCTGTCTCCAG
TAGTGTAGGAGCTGTTCGGTCTGGAAACCTAACATTTATGGTGGGAAGAGTTGAAGATGAATTTGCAGCTTCCCAAGAGT
TGCTGGAGTGTGTGGGCTCCAATGTGCTACACTGTGGAGCTGTTGGGACTGGGCAGTCTGCAGAGATATGCAACAACATG
CTGTTGGCTCTAAGCATAATTGGAACCACTGAAGCTATGAACCTTGGAATCAGGTCAGGCCTTGGCCCAAAACTATTGGC
TAAAATCCTAAATATGACCTCTGGACAATGCTGGTCCAGGGACACTTACAACCCTGTACCTGGAGTTATTCATGGAATCC
CCTCACCTAATAGCTACCAAGGTGGATTTGAAACAACACTAATGGCTAAGGATCTGGGATTGGCTCAAGACTCTGCCACC
AGCACCAAGACCCCAATTCTCTTAGGAAGCCTGGCCCATCAGATATACAGAATGATGTGTTCAAAGGGCTACTCAAAGAA
AGACTTCTCATCTGTT

Alignment

ORF - retro_mmus_2360 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.03 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMKHGYPLILYDVFPDVCKEFKEAGEQVASSPAEVAEKADRIITMLPSSMNAVEVYSGANGILKK---VK
          LMKHGYPLIL.DVFP.VCKEFKEAGEQV.SSP.EV..KAD.IITMLPSSMN.VEVYSGAN.I......VK
Retrocopy LMKHGYPLILCDVFPGVCKEFKEAGEQVVSSPSEVDGKADSIITMLPSSMNSVEVYSGANRIXXXXXXVK

Parental  KGSLLIDSSTIDPSVSKELAKEVEKMGAVFMDAPVSGGVGAARSGNLTFMVGGVEDEFAAAQELLECMGS
          .GSLLIDSSTIDPSVSKELAKEVEKMGAVFMD.PVS..VGA.RSGNLTFMVG.VEDEFAA.QELLEC.GS
Retrocopy NGSLLIDSSTIDPSVSKELAKEVEKMGAVFMDSPVSSSVGAVRSGNLTFMVGRVEDEFAASQELLECVGS

Parental  NVVYCGAVGTGQSAKICNNMLLAISMIGTAEAMNLGIRSGLDPKLLAKILNMSSGRCWSSDTYNPVPGVM
          NV..CGAVGTGQSA.ICNNMLLA.S.IGT.EAMNLGIRSGL.PKLLAKILNM.SG.CWS.DTYNPVPGV.
Retrocopy NVLHCGAVGTGQSAEICNNMLLALSIIGTTEAMNLGIRSGLGPKLLAKILNMTSGQCWSRDTYNPVPGVI

Parental  HGVPSSNNYQGGFGTTLMAKDLGLAQDSATSTKTPILLGSLAHQIYRMMCSKGYSKKDFSSV
          HG.PS.N.YQGGF.TTLMAKDLGLAQDSATSTKTPILLGSLAHQIYRMMCSKGYSKKDFSSV
Retrocopy HGIPSPNSYQGGFETTLMAKDLGLAQDSATSTKTPILLGSLAHQIYRMMCSKGYSKKDFSSV

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	0.02 RPM	36.49 RPM
SRP007412_cerebellum	0.00 RPM	45.55 RPM
SRP007412_heart	0.03 RPM	155.15 RPM
SRP007412_kidney	0.17 RPM	293.29 RPM
SRP007412_liver	0.03 RPM	240.07 RPM
SRP007412_testis	0.09 RPM	23.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2360 was not detected

EST

No EST(s) were mapped for retro_mmus_2360 retrocopy.

TSS

No TSS is located nearby retro_mmus_2360 retrocopy 5' end.

Lab

retro_mmus_2360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360 ,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,