RetrogeneDB ID: retro_mdom_1455

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:134132620..134134104(+)
• Located in intron of: ENSMODG00000000439

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLD
• Ensembl ID: ENSMODG00000016316
• Aliases: None
• Description: dihydrolipoamide dehydrogenase [Source:HGNC Symbol;Acc:2898]

Sequence

>retro_mdom_1455
AGAGGTCATTTCAGTTGAATACCTCATGGCCTACCAGGGATTTTTGCAGTGCCTCTGAGGACTTATGCAGATCAACCAAT
TGATGCTTATGTAAAGTCATAGGTTCTGGTCCTGGAGGATATGTTGCTGCTATTAAAGCTGCTCAACTTGACTTTAAGAG
AGTCTGTGTTGAAAAAAATGAAGCACTTGGTGGAACTTGTTTGAATGTTGGGTATATTCCTTCCAAAGCTTTATTGAATA
ACTCACATTTTTATCATTTGACTCATAAAGATTTTGCCTCTAGAGGAATTGAAATTTCAGAAATCCATTTGAATTTAGAG
AAGATGATGGAGCAAAAGCATGGTGCAGTAAAGGCTTTAACTGGTGGAATTGCTTACTTATTTAAGCAAAATAAGGTTAC
CCATGTGGATGGATTTGGAAAGATAACAGGCAAAAATCATGTTACAGCAACAAAATCTGATGGCAGCTCTTAGGTTATCA
ATACAAAGAACATTCTCATAGCCACGGTTTCAAAAGTTGCTCCCTTTCCTGGAATCATGATTGATGAAGATACAATTGTA
TCATCAACAGGTGCTTTATTCTTAAAAAAAGTTCCAGAAAAGATGATTATCATTGGTGCAGGAGTAATAGGTGTGGAACT
GGGTTCAGTTTGGCAATGACTTGGTTATGATGTGACAGCAGTTGAGTTCTTGGGTCATGTTGGTGGCATGGGAATTGATA
TGGAAATTTCATAAAATTTTCAGCAAATTCTTCAAAAACAGGGATTTAAATTTAAACTAAATACTAAAGTTACTGGGGCT
ACCAAGAAACCAGATGGAAAGATTGATGTAGCAATTGAAGCTGCTTCTGGTTGAAAAGCTGAAGTTATCACTTGTGGTTT
ACTCTTGGTTTGTATTGACCAACGACCCTTCACCAAACATCTGGGACTGGAAGAACTTGGAATTGAGCTAGATCCCAAAG
GTAGAATCCCAGTCAATACCAGATTCCAAACCAAAATTCCAAATATCTATTCCATCGGAGATGTAATTGCTGGCCCCATG
TTAGCTCACAAAGCAGAAGACGAAGGCATTATTTGCATTGAAGGGATGGCTGGTGGTGCTGTACACATTGACTACAATCG
TGTGCCTTCAGTGATCTATACACATCCTGAAGCTGCATGGGTTGGTAAATCAGAGGAGCAATTCAAAGAAGAGGGTATTG
AGTACAAAGTTGAAAAGTTTCCTTTTGCTGCTAATAGCAGAGCTAAGACTGATGCTGACACTGATGGCATCGTGAAGATC
CTTGGTCAGAAATCAACAGACAGAATATTGGGAGCACATATTCTAGGAGCAGGTGCCGAGGAAATGGTTAATGAAGCTGC
ACTTATCTTGGAATATGGAGCATCCTGTGAAGATGTTGCAAGAGTTTGTTATGCCCATCCAACTGTATCAGAAGCTTTCA
GGGAAGCAAACCTAGCTGCATCTTTTGTCAAAGTGATCAACTTT

Alignment

ORF - retro_mdom_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGHFSRIPHGLPGIFAVPLRTYADQPIDADVT-VIGSGPGGYVAAIKAAQLGFKTVCVEKNETLGGTCLN
          RGHFS.IPHGLPGIFAVPLRTYADQPIDA.V..VIGSGPGGYVAAIKAAQL.FK.VCVEKNE.LGGTCLN
Retrocopy RGHFS*IPHGLPGIFAVPLRTYADQPIDAYVK<VIGSGPGGYVAAIKAAQLDFKRVCVEKNEALGGTCLN

Parental  VGCIPSKALLNNSYFYHLAHKDFASRGIEISEIRLNLEKMMEQKRGAVKALTGGIAHLFKQNKVTRVDGF
          VG.IPSKALLNNS.FYHL.HKDFASRGIEISEI.LNLEKMMEQK.GAVKALTGGIA.LFKQNKVT.VDGF
Retrocopy VGYIPSKALLNNSHFYHLTHKDFASRGIEISEIHLNLEKMMEQKHGAVKALTGGIAYLFKQNKVTHVDGF

Parental  GKITGKNQVTATKSDGSSQVINTKNILIATGSEVAPFPGITIDEDTIVSSTGALSLKKVPEKMIVIGAGV
          GKITGKN.VTATKSDGSS.VINTKNILIAT.S.VAPFPGI.IDEDTIVSSTGAL.LKKVPEKMI.IGAGV
Retrocopy GKITGKNHVTATKSDGSS*VINTKNILIATVSKVAPFPGIMIDEDTIVSSTGALFLKKVPEKMIIIGAGV

Parental  IGVELGSVWQRLGSDVTAVEFLGHVGGMGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKPDGKIDVAI
          IGVELGSVWQ.LG.DVTAVEFLGHVGGMGIDMEIS.NFQ.ILQKQGFKFKLNTKVTGATKKPDGKIDVAI
Retrocopy IGVELGSVWQ*LGYDVTAVEFLGHVGGMGIDMEIS*NFQQILQKQGFKFKLNTKVTGATKKPDGKIDVAI

Parental  EAASGGKAEIITCDLLLVCIGRRPFTKNLGLEEFGIELDPKGRIPVNTRFQTKIPNIYAIGDVIAGPMLA
          EAASG.KAE.ITC.LLLVCI..RPFTK.LGLEE.GIELDPKGRIPVNTRFQTKIPNIY.IGDVIAGPMLA
Retrocopy EAASG*KAEVITCGLLLVCIDQRPFTKHLGLEELGIELDPKGRIPVNTRFQTKIPNIYSIGDVIAGPMLA

Parental  HKAEDEGIICIEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGVEYKVGKFPFAANSRAKTNA
          HKAEDEGIICIEGMAGGAVHIDYN.VPSVIYTHPE.AWVGKSEEQ.KEEG.EYKV.KFPFAANSRAKT.A
Retrocopy HKAEDEGIICIEGMAGGAVHIDYNRVPSVIYTHPEAAWVGKSEEQFKEEGIEYKVEKFPFAANSRAKTDA

Parental  DTDGMVKILGQKSTDRILGAHILGAGAGEMVNEAALALEYGASCEDVARVCHAHPTVSEAFREANLAASF
          DTDG.VKILGQKSTDRILGAHILGAGA.EMVNEAAL.LEYGASCEDVARVC.AHPTVSEAFREANLAASF
Retrocopy DTDGIVKILGQKSTDRILGAHILGAGAEEMVNEAALILEYGASCEDVARVCYAHPTVSEAFREANLAASF

Parental  GKAINF
          .K.INF
Retrocopy VKVINF

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

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1455 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1455 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.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005312	1 retrocopy	retro_cpor_685,
Monodelphis domestica	ENSMODG00000016316	2 retrocopies	retro_mdom_1455 , retro_mdom_448,
Oryctolagus cuniculus	ENSOCUG00000014667	1 retrocopy	retro_ocun_437,
Ictidomys tridecemlineatus	ENSSTOG00000007445	1 retrocopy	retro_itri_1226,
Tursiops truncatus	ENSTTRG00000003989	1 retrocopy	retro_ttru_699,