RetrogeneDB ID: retro_mdom_268

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:323679979..323680405(+)
• Located in intron of: ENSMODG00000004087

Retrocopy information

• Ensembl ID: ENSMODG00000024072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003811
• Aliases: None
• Description: None

Sequence

>retro_mdom_268
ATGCCTCCTAAATTCAAGCGCCACCTAAATGATGATGATGTCACTGGCTCTGTGAAAAGTGAAAGGAGAAATCTTTTGGA
AGAAGATTCAGATGAGGAAGAGGATTTTTTCCTGAGGGGCCCATCTGGACCAAAATTTGGACCCCGGAATGACAAAATCA
GGCATGTACAGAATCAGGTGGATGAAGTAATTGATGTCATGCAAGAGAATATTACAAAAGTGATTGAAAGAGGAGAGAGA
CTGGATGAGCTACAAGACAAATCAGAAAGCTTATCAGATAATGCAACAGCTTTTAGTAACAGATCTAAACAGCTTCGAAG
GCAAATGTGGTGGCGTGGATGCAAAATGAAGGCCATCATGGCTCTGGTTGCTGTTATCCTTTTGCTGGTGATTATCATTC
CTATTGTCCTGAAATATCGGTCTTGA

Alignment

ORF - retro_mdom_268 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MPPKFKRHLNDDDVTGSVKSERRNLLEEDSDEEEDFFLRGPSGPKFGPRNDKIRHVQNQVDEVIDVMQEN
          MPPKFKRHLNDDDVTGSVKSERRNLLEEDSDEEEDFFLRGPSGPKFGPRNDKIRHVQNQVDEVIDVMQEN
Retrocopy MPPKFKRHLNDDDVTGSVKSERRNLLEEDSDEEEDFFLRGPSGPKFGPRNDKIRHVQNQVDEVIDVMQEN

Parental  ITKVIERGERLDELQDKSESLSDNATAFSNRSKQLRRQMWWRGCKMKAIMALVAVILLLVIIIPIVLKYR
          ITKVIERGERLDELQDKSESLSDNATAFSNRSKQLRRQMWWRGCKMKAIMALVAVILLLVIIIPIVLKYR
Retrocopy ITKVIERGERLDELQDKSESLSDNATAFSNRSKQLRRQMWWRGCKMKAIMALVAVILLLVIIIPIVLKYR

Parental  S
          S
Retrocopy S

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_268 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_268 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 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016956	1 retrocopy	retro_amel_1457,
Choloepus hoffmanni	ENSCHOG00000000124	4 retrocopies	retro_chof_2225, retro_chof_2402, retro_chof_513, retro_chof_58,
Felis catus	ENSFCAG00000013371	1 retrocopy	retro_fcat_1167,
Macropus eugenii	ENSMEUG00000011226	13 retrocopies	retro_meug_1053, retro_meug_115, retro_meug_1257, retro_meug_1406, retro_meug_1489, retro_meug_1587, retro_meug_163, retro_meug_2075, retro_meug_2154, retro_meug_319, retro_meug_386, retro_meug_569, retro_meug_75,
Monodelphis domestica	ENSMODG00000003811	1 retrocopy	retro_mdom_268 ,
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273,
Mustela putorius furo	ENSMPUG00000015609	1 retrocopy	retro_mputfur_315,
Oryctolagus cuniculus	ENSOCUG00000015967	1 retrocopy	retro_ocun_844,
Otolemur garnettii	ENSOGAG00000026745	1 retrocopy	retro_ogar_3369,
Pteropus vampyrus	ENSPVAG00000014342	1 retrocopy	retro_pvam_97,
Sorex araneus	ENSSARG00000001709	2 retrocopies	retro_sara_234, retro_sara_79,
Sarcophilus harrisii	ENSSHAG00000017179	2 retrocopies	retro_shar_584, retro_shar_747,
Tupaia belangeri	ENSTBEG00000010829	2 retrocopies	retro_tbel_2607, retro_tbel_4488,
Vicugna pacos	ENSVPAG00000007424	1 retrocopy	retro_vpac_570,