RetrogeneDB ID: retro_mdom_1541

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:160485574..160486334(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000020726
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PACRGL
• Ensembl ID: ENSMODG00000000641
• Aliases: None
• Description: PARK2 co-regulated-like [Source:HGNC Symbol;Acc:28442]

Sequence

>retro_mdom_1541
TCAGGAGCCAACACTAAGAAAACAAGAATGCAGAAATCAGAGAGATATGGAAGCCTCCAGATGAGAAACAAGAGTGACAG
GAAACTATGAACAAAGAATATCATCAGGTTCCCAAGAAAAACATAGATCTGTAGTAGATGAAAACAAGTTACTACCTTCC
AAGAATTCTCCAGATTCTGTAAGGAAACCTCACCCTCGACCAAGTGATAAGCTTAATCCTAAAACTATTGACCCGTTTGG
TGATCAAACCACAAGCTCCATCTGCTTTTGCTGCTTTTTACTCTAAAGGAGGTATTCCTCGCAGGTTGGTACATAATGGT
TCAGTAAAACACAAATTACAGTGGGATTGTCTTCCTGAAACTCTTCCATTTGATCCTCTTTTTATTACTTTAGCAGAGGA
ACTAAGAGAGACTAAACATCCCTACAGATTTTTTTCAAAGGAAGATTTTAAAGAATTACTTTTGGTTGAAGGTGCTACTA
AAAAAACTGTGCCCCTGTTACCTAGACAGATTCCAGTGTTGAAGGCAGCTCTGACACATTTGGATGGTGAAGTGTTTAAA
GGGGATTGAATGCTTTAGTACAGTTGAGTGGTGGTGTTGGGCCTCCTCCAAATGATCATCTGAAGCACTTGCTTACAAGT
CTTTCAAAGAGACTAATGGAAAAGAAATTCAAAGAGCCAATCACCAGTGCTTTACAACATGGTGGAAGTGGCAGCCTTAT
GATTATCAAAGCTAAAATTCCAACCTATTGTTCCATCTGC

Alignment

ORF - retro_mdom_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGANSKKTRMQKSESHGSLQMRN-RVTGNYEQRISSGSQEKHRSVVHQNKLLPSKNSPDSVRKPHPRPSD
          SGAN.KKTRMQKSE..GSLQMRN.RVTGNYEQRISSGSQEKHRSVV..NKLLPSKNSPDSVRKPHPRPSD
Retrocopy SGANTKKTRMQKSERYGSLQMRN>RVTGNYEQRISSGSQEKHRSVVDENKLLPSKNSPDSVRKPHPRPSD

Parental  KLNPKTIDPFGDQ-PRAPSAFAAIYSKGGIPCRLVH-GSVKHKLQWDCLPETLPFDPLLITLAEGLRETK
          KLNPKTIDPFGDQ.P.APSAFAA.YSKGGIP.RLVH.GSVKHKLQWDCLPETLPFDPL.ITLAE.LRETK
Retrocopy KLNPKTIDPFGDQ>PQAPSAFAAFYSKGGIPRRLVHNGSVKHKLQWDCLPETLPFDPLFITLAEELRETK

Parental  HPYTFVSKEGFKELLLVEGATEKTVPLLPRLIPVLKAALTHSDGEVFE-RGLNALVQLSGVVGPSLNDHL
          HPY.F.SKE.FKELLLVEGAT.KTVPLLPR.IPVLKAALTH.DGEVF..RGLNALVQLSG.VGP..NDHL
Retrocopy HPYRFFSKEDFKELLLVEGATKKTVPLLPRQIPVLKAALTHLDGEVFK<RGLNALVQLSGGVGPPPNDHL

Parental  KHLLTSLSKRLMDKKFKEPITSALQKLEQHGGSGSLMIIKAKIPTYCSIC
          KHLLTSLSKRLM.KKFKEPITSALQ....HGGSGSLMIIKAKIPTYCSIC
Retrocopy KHLLTSLSKRLMEKKFKEPITSALQ----HGGSGSLMIIKAKIPTYCSIC

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_1541 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1541 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541 , retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866,