RetrogeneDB ID: retro_mdom_414

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:460658103..460659069(+)
• Located in intron of: ENSMODG00000012766

Retrocopy information

• Ensembl ID: ENSMODG00000012781
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSMODG00000000533
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_mdom_414
TTGTTGACAGCAACACCTGGCCGACTTCTGGACCACATGCAAAATACCCCAGGATTTATGTTTAAAAACCTGCAATGTCT
TGTTATGGGTGAGGCTGACCGAATTCTTGAGGTTGGGTTTGAGGAAGAAATGAAACAGATCATCAAACTTTTGCCAAAAT
GCAGACAAACAATGCTCTTTTCTGCCACACAAACTCGTAAGGTAGAAGATCTGGCAAAGATTTCCCTTAAAAAGGAACCA
TTATATGTTGGTGTTGATGACGATAAAGATACTGCAATAGTAGATGGTCTTGAACAGGGATATGTTGTTTGTCCATCTGA
GAAAAAATTCCTTCTACTCTTCACATTCCTTAAGAAGAACCAGAAGAAGAAACTGATGGTATTTTTTTCTTCATGTATGT
CAGTGAAATACCACTATGAGCTTCTCAACTACATTGATTTACCTATCATGGCCATTCATGGTAAGCAGAAGCAAAATAAG
CAGACAACTACATTCTTTCAGTTCTGCAATGCAGATTCTGGGATTTTGCTGTGTACAGATGTGGCTGCCAGAGGGCTAGA
TATTCCTGAAGTAGATTGGATTGTCCAGTATGACCCTCCAGATGATCCAAAGGAATATATCCATCGTGTAGGTAGAACAG
CCAGAGGTATAAACGGAAAAGGTCATGTTTTACTTATTTTGCGACCAGAAGAGTTGGGTTTTCTTCGTTACCTGAAGCAA
GCCAAGGTACCATTAAGTGAATTTGAATTTTCCTGGTCAAAAATTTCTGACATTCAGGCTCAGTTGGAAAAACTAATTGA
GAAGAACTATTTCCTTCATAAATCAGCACAGGAGGCATATAAATCCTATGTTCGAGCATATGATTCCCATTCTCTGAAGC
AAATCTACAATGTTAACAGCTTAAATTTACCTCTAGTTGCTTTATCATTTGGTTTCAAAGTGCCTCCATTTGTTAACCTG
AATCTG

Alignment

ORF - retro_mdom_414 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIVATPGRLLDHMQNTPGFMFKNLQCLVIDEADRILEVGFEEEMKQIIKLLPKRRQTMLFSATQTRKVED
          ...ATPGRLLDHMQNTPGFMFKNLQCLV..EADRILEVGFEEEMKQIIKLLPK.RQTMLFSATQTRKVED
Retrocopy LLTATPGRLLDHMQNTPGFMFKNLQCLVMGEADRILEVGFEEEMKQIIKLLPKCRQTMLFSATQTRKVED

Parental  LAKISLKKEPLYVGVDDDKDTATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYE
          LAKISLKKEPLYVGVDDDKDTA.VDGLEQGYVVCPSEK.FLLLFTFLKKN.KKKLMVFFSSCMSVKYHYE
Retrocopy LAKISLKKEPLYVGVDDDKDTAIVDGLEQGYVVCPSEKKFLLLFTFLKKNQKKKLMVFFSSCMSVKYHYE

Parental  LLNYIDLPVMAIHGKQKQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRV
          LLNYIDLP.MAIHGKQKQNK.TTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRV
Retrocopy LLNYIDLPIMAIHGKQKQNKQTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRV

Parental  GRTARGINGRGHALLILRPEELGFLRYLKQAKVPLSEFEFSWSKISDIQAQLEKLIEKNYFLHKSAQEAY
          GRTARGING.GH.LLILRPEELGFLRYLKQAKVPLSEFEFSWSKISDIQAQLEKLIEKNYFLHKSAQEAY
Retrocopy GRTARGINGKGHVLLILRPEELGFLRYLKQAKVPLSEFEFSWSKISDIQAQLEKLIEKNYFLHKSAQEAY

Parental  KSYVRAYDSHSLKQIYNVNSLNLPLVALSFGFKVPPFVDLSI
          KSYVRAYDSHSLKQIYNVNSLNLPLVALSFGFKVPPFV.L..
Retrocopy KSYVRAYDSHSLKQIYNVNSLNLPLVALSFGFKVPPFVNLNL

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	0.95 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.60 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.79 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_414 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_414 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 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221, retro_chof_1539, retro_chof_1636, retro_chof_2416, retro_chof_2418, retro_chof_721,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414 ,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,