RetrogeneDB ID: retro_mdom_254

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:31302336..31303890(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025196
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSMODG00000008641
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_mdom_254
ATGCTGCGTCTCTTGGCCCCCAGATTATCCAGGCTTTGTACAGGGGTTGCTCCCTACTCCTCTGCTGCATCTCTTCCAAA
CCCTGTGCTACAGCCAGAAGTCCGATATGACAAACTCTTCATCAATAATGAGTGGAGGGATGCAGTCAGCAAAAAGACAT
TCCCAACAGTCAATCCCTCAACAGGAGAGGTCATCACTCATGTGGCTGAAGGAGATAAGGCAGATGTAGACTTGGCTGTG
AAAGCTGCCCGGGAAGCCTTTCGGCTAGGGTCTCCATGGCGACAGTTGGATGCTTCCGAGAGGGGCAGGTTACTTTATCG
CCTGGCTGACCTAGTAGAGAGAGATCGCATCTATCTGGCCTCACTAGAGACCTTGGACAATGGAAAGCCTTTCCAAGAAT
CCTATGTTCTGGACCTCGATGAAGTCATTAAGGTGTATCGGTACTTTGCGGGCTGGGCAGACAAATTCCATGGGAAGACT
ATCCCTATGGATGGAGAGCTCTTCTGCTACACAAGGCATGAGCCCATTGGGGTGTGTGGCCAGATTATTCCATGGAACTT
TCCTCTGGTCATGCAAGGCTGGAAACTTGCCCCAGCCCTGGCAGCTGGCAATACTGTGGTTATGAAGGTGGCTGAACAGA
CCCCGCTGTCCGCCTTGTATCTTGCCTCCTTGATCAAAGAAGCTGGCTTTCCTCCTGGCGTAGTAAACATCATCACGGGC
TATGGACCTACGGCAGGGGCTGCTGTGGCCCAACACATGGACATTGATAAGGTGGCCTTTACTGGCTCCACAGAGGTTGG
CCATCTGATCCAGAAGGCGGCAGGGGACTCTAACCTGAAGAGGGTCACCCTGGAGCTGGGTGGGAAGAGCCCCAGTATCG
TCCTGGCAGATGCAGACATGAACCATGCTGTAGAACAATGCCACGAAGCACTCTTCTTCAACATGGGCCAGTGCTGCTGT
GCTGGCTCTCGGACCTTCGTGGAAGACTCCATCTATGATGAATTTCTTGAAAGAACTGTAGAAAAAGCCAAGAAGAGGAA
AGTTGGGAATCCCTTTGAGCTTGACACCCAGCAAGGGCCCCAGATAGACAAGGAACAGTTTGAAAAAATCCTGGGTTACA
TCCAAGTAGGCCAGAAAGAAGGTGCCAAATTGATGTGTGGGGGAGAACGCTTTGGGGAGAAAGGTTTCTTCATCAAGCCC
ACTGTCTTTGGCAATGTACAAGACAACATGCGGATTGCCAAGGAGGAGATCTTTGGACCCGTGCAGCCTGTGTTCAAATT
CAAAAAGATCAGTGAGATTATTGAGAGGGCCAATGATACCAAGTATGGGTTAGCAGCAGCTGTCTTCACCAAGGACCTGG
ACAAGGCTATGTATCTGACCCAAGCCCTGCAAGCTGGAACAGTGTGGGTCAATACCTATAACATTGTAACATGTCACACT
CCTTTTGGAGGGTTCAAGGAATCTGGAAATGGGAGAGAGCTAGGGGAAGATGGGCTCAGAGAATATGTAGAAGTAAAGAC
TGTAACAATCAAAATTCCTCAGAAAAATTCATGA

Alignment

ORF - retro_mdom_254 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.75 %
• Parental protein coverage: 95.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSPTLNLEIKYTKIFINNEWQNSESGRVFPVYNPATGEQVCEVQEADKADIDKAVRAARLAFSLGSVWR
          LP.P.L..E..Y.K.FINNEW....S...FP..NP.TGE....V.E.DKAD.D.AV.AAR.AF.LGS.WR
Retrocopy LPNPVLQPEVRYDKLFINNEWRDAVSKKTFPTVNPSTGEVITHVAEGDKADVDLAVKAAREAFRLGSPWR

Parental  RMDASERGRLLDKLADLVERDRAVLSTMESLNGGKPFLQAFYVDLQGVIKTLRYYAGWADKIHGMTIPVD
          ..DASERGRLL..LADLVERDR..L...E.L..GKPF......DL..VIK..RY.AGWADK.HG.TIP.D
Retrocopy QLDASERGRLLYRLADLVERDRIYLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKFHGKTIPMD

Parental  GDYFTFTRHEPIGVCGQIIPWNFPLLMFAWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGV
          G..F..TRHEPIGVCGQIIPWNFPL.M..WK.APAL..GNTVV.K.AEQTPLSALY...LIKEAGFPPGV
Retrocopy GELFCYTRHEPIGVCGQIIPWNFPLVMQGWKLAPALAAGNTVVMKVAEQTPLSALYLASLIKEAGFPPGV

Parental  INILPGYGPTAGAAIASHVGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAV
          .NI..GYGPTAGAA.A.H..IDK.AFTGSTEVG.LIQ.AAG.SNLKRVTLELGGKSP.I..ADAD...AV
Retrocopy VNIITGYGPTAGAAVAQHMDIDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADADMNHAV

Parental  EQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELI
          EQ.H...FFN.GQCC.AGSR.FVE.SIY.EF..R.VE.AK.R.VG.PF...T.QGPQIDK.Q..KIL..I
Retrocopy EQCHEALFFNMGQCCCAGSRTFVEDSIYDEFLERTVEKAKKRKVGNPFELDTQQGPQIDKEQFEKILGYI

Parental  QSGVAEGAKLECGGKGLGHKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTLDEVIERANNSDLGL
          Q.G..EGAKL.CGG...G.KGFFI.PTVF.NV.D.MRIAKEEIFGPVQ....FK...E.IERAN....GL
Retrocopy QVGQKEGAKLMCGGERFGEKGFFIKPTVFGNVQDNMRIAKEEIFGPVQPVFKFKKISEIIERANDTKYGL

Parental  VAAVFTNDINKALTVSAAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGECGLREYSEVKTVTIKIPQ
          .AAVFT.D..KA.....A.QAGTVW.N.YN......PFGGFK.SGNGRE.GE.GLREY.EVKTVTIKIPQ
Retrocopy AAAVFTKDLDKAMYLTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLREYVEVKTVTIKIPQ

Parental  KNS
          KNS
Retrocopy KNS

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	39.45 RPM
SRP007412_cerebellum	0.00 RPM	12.73 RPM
SRP007412_heart	0.00 RPM	18.74 RPM
SRP007412_kidney	0.00 RPM	6.58 RPM
SRP007412_liver	0.00 RPM	10.57 RPM
SRP007412_testis	0.00 RPM	20.82 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_254 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_254 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106,
Dasypus novemcinctus	ENSDNOG00000010541	1 retrocopy	retro_dnov_2235,
Erinaceus europaeus	ENSEEUG00000012262	1 retrocopy	retro_eeur_15,
Monodelphis domestica	ENSMODG00000008641	1 retrocopy	retro_mdom_254 ,
Pan troglodytes	ENSPTRG00000007113	1 retrocopy	retro_ptro_118,
Sorex araneus	ENSSARG00000012720	1 retrocopy	retro_sara_40,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111,
Tarsius syrichta	ENSTSYG00000004549	1 retrocopy	retro_tsyr_8,
Tursiops truncatus	ENSTTRG00000002361	1 retrocopy	retro_ttru_932,