RetrogeneDB ID: retro_mdom_360

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:280225944..280226408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPRD1A
• Ensembl ID: ENSMODG00000000399
• Aliases: None
• Description: regulation of nuclear pre-mRNA domain containing 1A [Source:HGNC Symbol;Acc:25560]

Sequence

>retro_mdom_360
GCTATTTGGGAAGAAAGGTCTGTTTATGCAAATGATGTATTAGAACACCTTAGACAACCTTTCTATAGTGATATGAAGTC
TAGAAAGAGTTCATATGAACAAATAAAGGTGGATGAGAATGAAAATTGTTCATCTCTAGGATAACCAAGTGAACCTCCAC
AGACTATAGATCTCATTAGAGCCTCACAAGAACTTGAAAATGCAGCCTCAGGTGATGCAGCAGTTCATGAGAGAATAGCT
TCTTTGCCTGTTGAAGTCCAAGATGTATCTCTGCTAGACAAAATAACAGATAAAGAATCAGGAGAACAGCTTTCCAGATG
GTAGATGATGCATTCATGTTCTTGGCAGAGTACAATGGTTAATAGGCAGCAGAAATAGATGATAGGAAGCAACTAACTTG
AATGTTATCAGATTTTCTTCATTGTCAAAAAGAGGCCCTTGCATAGAAAGAACATAAACTGGAA

Alignment

ORF - retro_mdom_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 57.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIWEERSVYENDVLEQLRQALYGDKKSRKRSYEQIKVDENENCSSLGSPSEPPQTIDLIRALQELENAAS
          .IWEERSVY.NDVLE.LRQ..Y.D.KSRK.SYEQIKVDENENCSSLG.PSEPPQTIDLIRA.QELENAAS
Retrocopy AIWEERSVYANDVLEHLRQPFYSDMKSRKSSYEQIKVDENENCSSLG*PSEPPQTIDLIRASQELENAAS

Parental  GDAAVHQRIASLPVEVQDVSLLDKITDKESGEQLSK-MVDDACMLLADYNGRLAAEIDDRKQLTRMLSDF
          GDAAVH.RIASLPVEVQDVSLLDKITDKESGEQLS..MVDDA.M.LA.YNG..AAEIDDRKQLT.MLSDF
Retrocopy GDAAVHERIASLPVEVQDVSLLDKITDKESGEQLSR<MVDDAFMFLAEYNG**AAEIDDRKQLT*MLSDF

Parental  LRCQKEALAEKEHKLE
          L.CQKEALA.KEHKLE
Retrocopy LHCQKEALA*KEHKLE

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_360 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_360 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007025	1 retrocopy	retro_eeur_245,
Gorilla gorilla	ENSGGOG00000007369	1 retrocopy	retro_ggor_1237,
Macaca mulatta	ENSMMUG00000018777	1 retrocopy	retro_mmul_1562,
Monodelphis domestica	ENSMODG00000000399	1 retrocopy	retro_mdom_360 ,
Nomascus leucogenys	ENSNLEG00000006228	1 retrocopy	retro_nleu_1323,
Pongo abelii	ENSPPYG00000009111	1 retrocopy	retro_pabe_1352,
Pan troglodytes	ENSPTRG00000009974	1 retrocopy	retro_ptro_1106,
Vicugna pacos	ENSVPAG00000001641	1 retrocopy	retro_vpac_62,