RetrogeneDB ID: retro_mdom_1646

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:37837289..37837876(-)
• Located in intron of: None

Retrocopy information

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

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_1646
TCAGGAGCCAACACTAAGAAAGCAAGAATACAGAAATCAGAGAGTTCTGAAAGCCTCCAGACAAGAAACAGAGAGACAGG
AAAATATGAACAAAGACTATCATCAGGTTCCCAAGAAAAACATAATCTGTATTTCATCAAAACAAGTTATTACTTTTCAA
GAATTCTCCAGATTTTGTAAGGAAACCTCACCCTCCACAGAATGATAAGCTTAATCCTAAAACTGTTGACCCATTTTGTG
ATCAGCCACAAACTTTGTCTACTTTTGCTGCTGTTTACTCTAAAGGAGGTATTCCTTGCAGGTTGGTACATCATTCAATA
AAACACAAATTACAGTGGGACTGTCTTCCTGAAACTCTTTGATTTGAAACTCTTCTTATTACTTTAGTAGAGGACCTAAG
AGACACTAAATATCCATACACATTTGTATCAAGAGAAGGTTTTAAAGAATTACTTTTGGTTGAAGGTGTTACTGAAAAAA
CAGTGTCCCTGATATCTAGATTGATTCCAGTGTTGAAGGCAGCTCTGACACATTCAGATGGTGAAGTGTTTGAATGGGGA
TTGAATGTTTTAATACAGTAGAGTGGT

Alignment

ORF - retro_mdom_1646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 75.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGANSKKTRMQKSESHGSLQMRNRVTGNYEQRISSGSQEKHR-SVVHQNKLLPSKNSPDSVRKPHPRPSD
          SGAN.KK.R.QKSES..SLQ.RNR.TG.YEQR.SSGSQEKH..SV.HQNKLL..KNSPD.VRKPHP...D
Retrocopy SGANTKKARIQKSESSESLQTRNRETGKYEQRLSSGSQEKHN<SVFHQNKLLLFKNSPDFVRKPHPPQND

Parental  KLNPKTIDPFGDQPRAPSAFAAIYSKGGIPCRLVHGSVKHKLQWDCLPETLPFDPLLITLAEGLRETKHP
          KLNPKT.DPF.DQP...S.FAA.YSKGGIPCRLVH.S.KHKLQWDCLPETL.F..LLITL.E.LR.TK.P
Retrocopy KLNPKTVDPFCDQPQTLSTFAAVYSKGGIPCRLVHHSIKHKLQWDCLPETL*FETLLITLVEDLRDTKYP

Parental  YTFVSKEGFKELLLVEGATEKTVPLLPRLIPVLKAALTHSDGEVFERGLNALVQLSG
          YTFVS.EGFKELLLVEG.TEKTV.L..RLIPVLKAALTHSDGEVFE.GLN.L.Q.SG
Retrocopy YTFVSREGFKELLLVEGVTEKTVSLISRLIPVLKAALTHSDGEVFEWGLNVLIQ*SG

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_1646 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1646 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,