RetrogeneDB ID: retro_mdom_277

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:188039836..188040778(+)
• Located in intron of: ENSMODG00000001626

Retrocopy information

• Ensembl ID: ENSMODG00000018837
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004900
• Aliases: None
• Description: None

Sequence

>retro_mdom_277
ATGGAGGACAGGAAGCGCCTTGCTTATTCAATCATTCAGTTCCTGCATGACCAAGTGAAACATGGAAGACTCTCTTCTGA
TGCCCAGGAGAGTTTGGAAGCTTCAATCCAGTGCCTGGAGACAGCTTTTGAGGTGACTGTTGATGACCGACATCTAGCTG
TATCACAAACTCTGCCAGAAATATTTGAAGCTGCTATAGAAAGAGGAGAGGTGCGCAACATACACAAGAATTCTGAGCCC
ATCCCCACCATTGATAAAGAGACACCTGAAGCTGAAAGATTCAAAAGGAAAGGAAATGAACAAATGAAAAAGGAAAACTT
TGAAGAGGCAGTCTCTTTCTATGGAAAAGCAATTGAATTAAATCCAACCAATGCAGTGTATTTTTGCAACAGAGCTGCGG
CCTACAGCAAAATTGGAGATTATGCAGGTGCTATGAAAGACTGTGAAAGAGCCATTGGCATAGACCCCTACTACAGCAAA
GCCTATGGCAGAATGGGATTAGCACTTTTAAGTTTAAACAAGCACAAGGAGGCTGTGGGCTACTATAAGAAGGCCCTGGA
GCTGGACCCAGACAATGACATGTACAAAACAAACTTCAAGTTAGCTCAAAAGAAAATGAAAGAAACATCCGATGCTACAG
AAAACACTGGAGGCATTGACCTAGCTGGCTTACTGAGTAACCCAGGTCTGAGGAATATGGCATCAAACCTCATGAATAAT
CCTCAAGTACAGCAAGTTGTGTCTGGGGTAGCATCAAGTATCCAAAATCATTCTGGAGCTGCCAGAGGCAACCGTTCTCC
AAATAACATCTCCAACCTCCTCCAGGCAGGCCAGCATTTTGCTCAGCAGCTACAGCAACAAAATCCAGAGTTGATAGAAC
AGCTCAAAAACCAGATTAGGAGTCGAAGCTCCAAAACCAGCAATGATGATCAGAAGGAATGA

Alignment

ORF - retro_mdom_277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDKKRLAYSIIQFLHDQLHHGCLSPDAQESLEVAIQCLETAFGVTVEDRDLAVSQTLPQIFEAATGKKE
          MED.KRLAYSIIQFLHDQ..HG.LS.DAQESLE..IQCLETAF.VTV.DR.LAVSQTLP.IFEAA....E
Retrocopy MEDRKRLAYSIIQFLHDQVKHGRLSSDAQESLEASIQCLETAFEVTVDDRHLAVSQTLPEIFEAAIERGE

Parental  MPYIRRNSEPIPPSDEDTAEAERLKTEGNEQMKIENFEAAVSFYGKAIELNPANAVYFCNRAAAYSKLGN
          ...I..NSEPIP..D..T.EAER.K..GNEQMK.ENFE.AVSFYGKAIELNP.NAVYFCNRAAAYSK.G.
Retrocopy VRNIHKNSEPIPTIDKETPEAERFKRKGNEQMKKENFEEAVSFYGKAIELNPTNAVYFCNRAAAYSKIGD

Parental  YAGAVRDCERAIGIDPYYSKAYGRMGLALSSLNKHTEAVVYYKKALELDPDNDTYKSNLKIAEQKMKETP
          YAGA..DCERAIGIDPYYSKAYGRMGLAL.SLNKH.EAV.YYKKALELDPDND.YK.N.K.A..KMKET.
Retrocopy YAGAMKDCERAIGIDPYYSKAYGRMGLALLSLNKHKEAVGYYKKALELDPDNDMYKTNFKLAQKKMKETS

Parental  SPTGGTGGFDLAGLLNNPGFMSMASNLMNNPQVQQLMSGMISGGHNPLGGAGASPSPNDLASLIQA
          ..T..TGG.DLAGLL.NPG...MASNLMNNPQVQQ..SG..S...N..G.A....SPN....L.QA
Retrocopy DATENTGGIDLAGLLSNPGLRNMASNLMNNPQVQQVVSGVASSIQNHSGAARGNRSPNNISNLLQA

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	0.24 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	862.34 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_277 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_277 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005257	1 retrocopy	retro_amel_1169,
Equus caballus	ENSECAG00000010381	2 retrocopies	retro_ecab_723, retro_ecab_780,
Monodelphis domestica	ENSMODG00000004900	1 retrocopy	retro_mdom_277 ,
Mus musculus	ENSMUSG00000004937	1 retrocopy	retro_mmus_621,
Sarcophilus harrisii	ENSSHAG00000011900	1 retrocopy	retro_shar_39,