RetrogeneDB ID: retro_mdom_1069

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:499552581..499553525(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000358
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EXD2
• Ensembl ID: ENSMODG00000010228
• Aliases: None
• Description: exonuclease 3'-5' domain containing 2 [Source:HGNC Symbol;Acc:20217]

Sequence

>retro_mdom_1069
GTTGTTCCCAACGTCTCACGCGTGGAAAGGGTCCTCGGAGAGAGCGTGGCGATTGTGTCTGACAGGGAAGAATGGGAGAG
AGTTGAGTCTTTTCTCTGGGAGGAGTTGGAACAATGGCCAGTCCTTGGAATTGACTGTGAACGGGTACATGTGAAAGGCA
AAGCAAGACCTGTTTCACTCCTACAAACGGCTTCCCCTACTGGTTATCGCATTTTCATTAGTCTGCCTAAGCTGATCTCT
GGTGAAGCAGGTTTTCCCCAAGCCCTGGTGGATCTTTTAGAAGACAGCAGAACCTTAAAGGCTGGGGTTGGCTGTTGGGA
AGATGCCAGCAAGTCACTTCGGGAATATGATCTCACGCTGAGAGGATGTCTGGACCTCCGAAATCTGGCCATGAGACAGA
GGAGAGATTTGCTTCCAAATGGGCTTAGCCTGAAGTTCCTTGCTGAAACCGTACGCAGCTTTCCTCTGGACAGATCGCCT
CTTCTTCGTTCCAGCAATTGGGATGCTGAAGATCTCACTAAGGAACAGGTTGCTTATGCTGCTAGAGATGCTCAGATTTC
GGTGGCTCTCTTTCTTCGTCTTCTGCAATATCCTTTATCCATGAATTCAACCCAGAATGGACATAATGAAACCACTTGGG
AAAAAATATTGATGAAGTGCCAGGATCTTGTAGATCTTCCTTTCCATGGTAAAGGGAACAGCAGCAACATGAGAGAAGAA
AATTCCGGAAAAATGGAGGGCTCCCAGAAAACAAGAAACCTGGAATCTAGACCTGGCATGATGTCTTCAGGTGATCAGCA
AGGCAGGGACCCAGAAAACAGAAATCGAAGCCCCTCGGCAAGGGCCATTCTGCTCGGAAATCTCCACTCTATGATAACTG
CTTCTTACGTGCTCCTGGTGGACAGCCTCTATGCACGTGGGATAGAAGGAAAGCTCAGTGGTAT

Alignment

ORF - retro_mdom_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.24 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVPKVSQVERILRESVVIVSEREEWERVESFLWEELEQCPVLGIDCEWVNVKGKARPVSLLQMASPTGYC
          VVP.VS.VER.L.ESV.IVS.REEWERVESFLWEELEQ.PVLGIDCE.V.VKGKARPVSLLQ.ASPTGY.
Retrocopy VVPNVSRVERVLGESVAIVSDREEWERVESFLWEELEQWPVLGIDCERVHVKGKARPVSLLQTASPTGYR

Parental  ILIRLPKLISGEAGFPQTLVDLLEDSRILKVGVGCWEDASKLLREYDLTVRGCLDLRNLAMRQRRDLLPN
          I.I.LPKLISGEAGFPQ.LVDLLEDSR.LK.GVGCWEDASK.LREYDLT.RGCLDLRNLAMRQRRDLLPN
Retrocopy IFISLPKLISGEAGFPQALVDLLEDSRTLKAGVGCWEDASKSLREYDLTLRGCLDLRNLAMRQRRDLLPN

Parental  GLSLKFLAETILSFPLDKSPLLRSSNWDAEDLTKEQVAYAARDAQISVALFLHLLEYPLSMNSTQNGDNE
          GLSLKFLAET..SFPLD.SPLLRSSNWDAEDLTKEQVAYAARDAQISVALFL.LL.YPLSMNSTQNG.NE
Retrocopy GLSLKFLAETVRSFPLDRSPLLRSSNWDAEDLTKEQVAYAARDAQISVALFLRLLQYPLSMNSTQNGHNE

Parental  TTWEKILMKCQDLVDIPFHGKGNSSNTREENSGKMEGSQKTRNLKSRPGVMSSDDQQGRD-PRKQKSKPL
          TTWEKILMKCQDLVD.PFHGKGNSSN.REENSGKMEGSQKTRNL.SRPG.MSS.DQQGRD.PRKQKSKPL
Retrocopy TTWEKILMKCQDLVDLPFHGKGNSSNMREENSGKMEGSQKTRNLESRPGMMSSGDQQGRD<PRKQKSKPL

Parental  GKGYSARKSPLYDNCFLHAPDGQPLCTCDRRKAQWY
          GKG.SARKSPLYDNCFL.AP.GQPLCT.DRRKAQWY
Retrocopy GKGHSARKSPLYDNCFLRAPGGQPLCTWDRRKAQWY

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	61.86 RPM
SRP007412_cerebellum	0.00 RPM	110.99 RPM
SRP007412_heart	0.00 RPM	11.36 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	19.64 RPM
SRP007412_testis	0.00 RPM	70.91 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1069 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1069 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010228	1 retrocopy	retro_mdom_1069 ,