RetrogeneDB ID: retro_mdom_855

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:210319898..210320361(-)
• Located in intron of: ENSMODG00000010102

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC7
• Ensembl ID: ENSMODG00000007172
• Aliases: None
• Description: armadillo repeat containing 7 [Source:HGNC Symbol;Acc:26168]

Sequence

>retro_mdom_855
ATAGATCCAAAGCCTCAAGTTGTCTTAGAGGGAGGATGGCTAGAATACCTGAAGGCACTGCTCACCAAGTTCTAGGAGAC
AGCAAAACAAGAAGCCAAGGAGCAAATGCTATTGAATCTAGTAAAGTCTGCCCGTGATCCCAACAACTACCAGTATCCCC
CAGGAATTGAAGATGTTGAACTTATTCCTTGATGTACTATTGAGTGACAACAGTGATACATTAGTGGAATTTGTCATCAG
TGGCTTTTGCAACCTGTGCCTGGATAAAGTTAACAAAGAGTATATTCTACAGATGGGAGGCATCAAACCAATCAACAATT
GCCTCTACAGCCCCAATGAGGAGATAGTCATGTCAGTAGTCACAATACTCATGTTCCTGAGCACATCCCAGTCCATGTAG
GAACACATATCCATGCCAGTGGTGGAATGCTTATTATTTTGCTCTTCCTCTCTGCAACTAAGA

Alignment

ORF - retro_mdom_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.68 %
• Parental protein coverage: 80.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPKPRVVPEGGRLEYLQALVTEFQETASQEAKEQVLANLANFAYDPNNYQYL-RELQVLDLFLDVL-SE
          .DPKP.VV.EGG.LEYL.AL.T.F.ETA.QEAKEQ.L.NL...A.DPNNYQY...EL..L.LFLDVL.S.
Retrocopy IDPKPQVVLEGGWLEYLKALLTKF*ETAKQEAKEQMLLNLVKSARDPNNYQYP>QELKMLNLFLDVLLSD

Parental  DSDTLVEFAIGGLCNLCLDKVNKEYILQMGGVKPIINCLSSSNEETVMSAVTTLMFLSTSQSIQELTALP
          .SDTLVEF.I.G.CNLCLDKVNKEYILQMGG.KPI.NCL.S.NEE.VMS.VT.LMFLSTSQS..E....P
Retrocopy NSDTLVEFVISGFCNLCLDKVNKEYILQMGGIKPINNCLYSPNEEIVMSVVTILMFLSTSQSM*EHISMP

Parental  VVECMLRFSLSANKR
          VVEC.L..S.S...R
Retrocopy VVECLLFCSSSLQLR

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_855 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_855 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000007172	1 retrocopy	retro_mdom_855 ,
Ictidomys tridecemlineatus	ENSSTOG00000015164	1 retrocopy	retro_itri_455,