RetrogeneDB ID: retro_mdom_448

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:591723568..591724804(+)
• Located in intron of: None

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_448
AGAGGTCATTTCAGTCGAATACCTCATGGCCTACCAGGGATTTTTGCAGTGCCTCTGAGGACTTATGCAGATCAACCAAT
TGATGCTGATGTAACAGTCATAGGTTCTAGTCCTGGAGGATATGTTGCTGCTATTAAAGTTGCTCAACCTGGCTTTAAGA
CAGTCTGTGTTGAAAAAAATGAAACACTTGATGGAACTTGTTTGAATGTTGGATGTATTCCTTCTAAAGCTTTATTGAAT
AACTCACATTTTTATCATTTGACTCAAAAAGATTTTGCCTCTAGAGGAATTGAAATTTCAGAAATCCGCTTGAATTTAGA
GAAGATGATAGAGCAAAAGCGTGGTGCAGTAAAGGCTTTAACTGGTGGAATTGCTCATTTATTTAAGCAAAATAAGGTTA
CCTGTGTGGATGGATTTGGAAAGATAATGGGCAAAAATCAGGTTACAGCAACAAAATCTGATGGCAGCTCTTAGGTTATC
AATACAAAGAACATTCTCATAGCCACAGGTTCAGAAGTTGCTCCCTTTCCTGGAATCACGATTGATGAAGATACAATTGT
ATCATCAACAGGTGCTTTATCCTTAAAAAAAGTTCCAGAAAAGATGATTGTCATTGGTGCAGGAGTAATAGGTGTGGAAC
TGGGTTCAGTTTGGCAACGACTTGGTTCTGATGTGACAGCAGTTGAGTTCTTGGGTCATGTTGGTGGCATGGGAATTGAT
ATGGAAATTTCAAAAAATTTTCAGCGAATCCTTCAAAAACAAGGATTTAAATTTAAATTAAATACTAAAGTTACTGGGAC
TACCAAGAAACCAGATGGAAAGATTGATGTAGCAATTGAAGCTGCTTCTGGTGGAAAAGCTGAAGTTATCACTTGTGATT
TACTCTTGGTTTGTATTGGCTGACGACCCTTCACCAAAAATCTGAGACTGGAAGAACTTGGAATTGAGCTAGATCCCAAA
GGTAGAATCCCAGTCAATACCAGATTCCAAACCAAAATTCCAAATATCTATGCCATCGGAGATGTAATTGCTGGTCCCAT
GTTAGCTCACAATGCAGAAGATGAAGGCATTATTTGCATTGAAGGGATGGCTGGTGGTGCTGTACACATTAACTACAATT
GTGTGCCTTCAGTGATCTATACACATCCTGAAGTTGCATGGGTTGGTAAATCAGAGGAGCAATTAAAAGAAGAGGGTGTT
GAGTACAAAGTTGGAAAGTTGTGTTATGTCAGGAAT

Alignment

ORF - retro_mdom_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 83.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGHFSRIPHGLPGIFAVPLRTYADQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCVEKNETLGGTCLNV
          RGHFSRIPHGLPGIFAVPLRTYADQPIDADVTVIGS.PGGYVAAIK.AQ.GFKTVCVEKNETL.GTCLNV
Retrocopy RGHFSRIPHGLPGIFAVPLRTYADQPIDADVTVIGSSPGGYVAAIKVAQPGFKTVCVEKNETLDGTCLNV

Parental  GCIPSKALLNNSYFYHLAHKDFASRGIEISEIRLNLEKMMEQKRGAVKALTGGIAHLFKQNKVTRVDGFG
          GCIPSKALLNNS.FYHL..KDFASRGIEISEIRLNLEKM.EQKRGAVKALTGGIAHLFKQNKVT.VDGFG
Retrocopy GCIPSKALLNNSHFYHLTQKDFASRGIEISEIRLNLEKMIEQKRGAVKALTGGIAHLFKQNKVTCVDGFG

Parental  KITGKNQVTATKSDGSSQVINTKNILIATGSEVAPFPGITIDEDTIVSSTGALSLKKVPEKMIVIGAGVI
          KI.GKNQVTATKSDGSS.VINTKNILIATGSEVAPFPGITIDEDTIVSSTGALSLKKVPEKMIVIGAGVI
Retrocopy KIMGKNQVTATKSDGSS*VINTKNILIATGSEVAPFPGITIDEDTIVSSTGALSLKKVPEKMIVIGAGVI

Parental  GVELGSVWQRLGSDVTAVEFLGHVGGMGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKPDGKIDVAIE
          GVELGSVWQRLGSDVTAVEFLGHVGGMGIDMEISKNFQRILQKQGFKFKLNTKVTG.TKKPDGKIDVAIE
Retrocopy GVELGSVWQRLGSDVTAVEFLGHVGGMGIDMEISKNFQRILQKQGFKFKLNTKVTGTTKKPDGKIDVAIE

Parental  AASGGKAEIITCDLLLVCIGRRPFTKNLGLEEFGIELDPKGRIPVNTRFQTKIPNIYAIGDVIAGPMLAH
          AASGGKAE.ITCDLLLVCIG.RPFTKNL.LEE.GIELDPKGRIPVNTRFQTKIPNIYAIGDVIAGPMLAH
Retrocopy AASGGKAEVITCDLLLVCIG*RPFTKNLRLEELGIELDPKGRIPVNTRFQTKIPNIYAIGDVIAGPMLAH

Parental  KAEDEGIICIEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGVEYKVGKFPFAAN
          .AEDEGIICIEGMAGGAVHI.YNCVPSVIYTHPEVAWVGKSEEQLKEEGVEYKVGK.....N
Retrocopy NAEDEGIICIEGMAGGAVHINYNCVPSVIYTHPEVAWVGKSEEQLKEEGVEYKVGKLCYVRN

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	4.77 RPM	0.00 RPM
SRP007412_cerebellum	4.24 RPM	0.00 RPM
SRP007412_heart	33.89 RPM	0.00 RPM
SRP007412_kidney	18.44 RPM	0.00 RPM
SRP007412_liver	7.55 RPM	0.00 RPM
SRP007412_testis	2.36 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_448 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_448 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,