RetrogeneDB ID: retro_mdom_241

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:395831738..395832284(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024451
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSMODG00000013804
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]

Sequence

>retro_mdom_241
ATGGGGAATATATTTGCTAACTCCTTCAAGGGGCTCTTTGGCAGAAAAGAAATGAGGATTCTAATGGTTGGTCTGGATGC
TGCAGGAAAGACTACTATTTTGTACAAACTGAAGCTGGGTGAAATAGTAACTACTATTCCCACTATAGGTTTCAACGTAG
AAACTGTAGAATACAAAAACATTACCTTCACGGTGTGGGATGTAGGTGGCCAGGACAAAATCCGACCCTTATGGCGCCAT
TACTTCGAGAATACTCAAGGACTGATTTTTGTGGTTGACAGCAATGACAGAGAGCGAGTGGTTGAGGCCCGAGGAGAACT
GATGAGAATGTTGGCAGAGGAGGATCTTAGAAATGCCATCTTATTAGTGTTTGCTAACAAACGAGATCTTCCCAATGCCA
TGAATGCAGCTGAAATCACAGATAAACTCGGACTTCATTCTCTCCGTAACAGAAACTGGTACATCCAAGCCACCTGTGCC
ACTAGTGGGGATGGGCTCTATGAAGGACTGGACTGGTTGTCCAATCAGCTCCGAAACCAGAAATGA

Alignment

ORF - retro_mdom_241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          MGNIFAN.FKGLFG.KEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI.FTVWDVGG
Retrocopy MGNIFANSFKGLFGRKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNITFTVWDVGG

Parental  QGQIRPYGAITSEYQVRLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEIT
          Q..IRP......E....LIFVVDSNDRERV.EAR.ELMRMLAE..LR.A.LLVFANK.DLPNAMNAAEIT
Retrocopy QDKIRPLWRHYFENTQGLIFVVDSNDRERVVEARGELMRMLAEEDLRNAILLVFANKRDLPNAMNAAEIT

Parental  DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          DKLGLHSLR.RNWYIQATCATSGDGLYEGLDWLSNQLRNQK
Retrocopy DKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

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_241 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_241 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 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000000185	1 retrocopy	retro_mdom_1538,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241 ,
Monodelphis domestica	ENSMODG00000015229	1 retrocopy	retro_mdom_905,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,