RetrogeneDB ID: retro_mdom_1572

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:19696190..19697162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APMAP
• Ensembl ID: ENSMODG00000006313
• Aliases: None
• Description: adipocyte plasma membrane associated protein [Source:HGNC Symbol;Acc:13238]

Sequence

>retro_mdom_1572
TTATTTGAGAACCAGCTTATTGGTCCAGAGTCCATAGCAAATATTGGTGATGTTTTGTTTACTGGCACTGCTGATGGTCA
GATTGTAAACCTTGAAAATGAAGAAGTAATCACAATTGCCAGACTTGGTAAAGGCCCTTACAAAACAAGAGAAGATGAGC
CCATCTGTGGGAGACCTCTTGGAATATGAGTTGGGTCTAATGGTACTCTTTTTGTGGCAGATGCTTATCAGGGACTATTT
GAAGTAGAACCTAGTACAGGTAGAGTAAAACAGCTTTTGTCTTCCAAAACACCTATTGAGGGAAAGAAAATATCATTTGT
GAATGATCTGACAATTACTCAGGATGGGAGGAAAATTTATTTTACAGATTCTAGCAGTAAATGGCAAAGATGAGATTATC
TGCTCTTGGTTATGGAGGGTACAGATGATGGATAATTGCTAGAATATGATACTGTAACCAGAGAAGTAAAGATTTTAATA
GAAGGATTAAGCTTCCCCAATGGAGTTCAGCTGTCTCCTGCTGAAGATTTTGTTTTGGTGGCAGAAACTACTATGAAAAG
AATAAGAAGATTCTATGTGTCTGGGTTTATGAAGAGTGGGGCAGACATGTTTGTAGAAAACATGCCTGGTTTTCCAGATA
ACATTAGACCAAGCAGCGCTGGAGGATACTGGGTTGCCATGTCAACTGTTCGGCACAATCCTGAGTTTTTCTCTGTTGGA
TTTTTTATCAGAAAAAAAACATGAATTAAAAGATTAATTTTTAAGCTGTTAAGTCCAGAAACTGTGTCGAAGGTTGTACC
TCAATATAGCCTTGTCTTGGAACTTAGGGACAGTGGAACCTACCAGAGAAGCTTACATGTTCCCACTGGACAGGTTTTCA
GCTATATTAATGAAGTGCATGAACACGATGGACACCTTTACCTGGGTTCCTTTAGATCTCCTTTTCTTTGCACACTTAAC
ATTGATCTCCTC

Alignment

ORF - retro_mdom_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.2 %
• Parental protein coverage: 77.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFENQLIGPESIANIGDVLFTGTADGRIVKLENGEVITIARLGKGPCKTREDEPVCGRPLGIRVGPNGTL
          LFENQLIGPESIANIGDVLFTGTADG.IV.LEN.EVITIARLGKGP.KTREDEP.CGRPLGI.VG.NGTL
Retrocopy LFENQLIGPESIANIGDVLFTGTADGQIVNLENEEVITIARLGKGPYKTREDEPICGRPLGI*VGSNGTL

Parental  FVADAYQGLFEVEPSTGRVKQLLSSQTPIEGKKMSFVNDLTITQDGRKIYFTDSSSKWQRRDYLLLVMEG
          FVADAYQGLFEVEPSTGRVKQLLSS.TPIEGKK.SFVNDLTITQDGRKIYFTDSSSKWQR.DYLLLVMEG
Retrocopy FVADAYQGLFEVEPSTGRVKQLLSSKTPIEGKKISFVNDLTITQDGRKIYFTDSSSKWQR*DYLLLVMEG

Parental  TDDGRLLEYDTVTREVKVLMEGLRFPNGVQLSPAEDFVLVAETTMARIRRFYVSGLMKGGADMFVENMPG
          TDDG.LLEYDTVTREVK.L.EGL.FPNGVQLSPAEDFVLVAETTM.RIRRFYVSG.MK.GADMFVENMPG
Retrocopy TDDG*LLEYDTVTREVKILIEGLSFPNGVQLSPAEDFVLVAETTMKRIRRFYVSGFMKSGADMFVENMPG

Parental  FPDNIRPSSSGGYWVAMSTVRHNPGF-SMLDFLSEKPWIKRLIFKLLSPETVSKFVPRYSLVLELGDSGT
          FPDNIRPSS.GGYWVAMSTVRHNP.F.S...F......IKRLIFKLLSPETVSK.VP.YSLVLEL.DSGT
Retrocopy FPDNIRPSSAGGYWVAMSTVRHNPEFFSVGFFIXXXX*IKRLIFKLLSPETVSKVVPQYSLVLELRDSGT

Parental  YQRSLHDPTGQVVSYISEVHEHDGHLYLGSFRSPFLCTLNIDLL
          YQRSLH.PTGQV.SYI.EVHEHDGHLYLGSFRSPFLCTLNIDLL
Retrocopy YQRSLHVPTGQVFSYINEVHEHDGHLYLGSFRSPFLCTLNIDLL

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	30.99 RPM
SRP007412_cerebellum	0.00 RPM	40.15 RPM
SRP007412_heart	0.00 RPM	36.48 RPM
SRP007412_kidney	0.00 RPM	343.69 RPM
SRP007412_liver	0.00 RPM	674.68 RPM
SRP007412_testis	0.00 RPM	92.52 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1572 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1572 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006313	1 retrocopy	retro_mdom_1572 ,