RetrogeneDB ID: retro_mdom_1083

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:33614451..33615040(-)
• Located in intron of: ENSMODG00000028454

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGK2
• Ensembl ID: ENSMODG00000001260
• Aliases: None
• Description: serum/glucocorticoid regulated kinase 2 [Source:HGNC Symbol;Acc:13900]

Sequence

>retro_mdom_1083
GGAGTAGAGTTCTTTCACTTGAAATGCGAACACTGTTTCTTAGAACATTGAGCTTGAATCTATATGATACTGAGGTGGCT
GGTATGCTGGCTCCCTGCATTCTTTGAACATCATTTACAGGGACTTGAAACCAGAGGACATTCTCTTGGATTGCCAGCGC
CATGTTGTATCAACTTATTTTGGGCTTTGTAAAGAAGAAATGGAACTAGAAGAAATCACATCCAATTTATGTGGCATCCC
AAGTTATTTTGCTCCTGAAGCATTGAGAAAACAACCCTATGACTGAACATTAGAGTAGTGGTGTTTGGGGCGGTTTTGTA
GGAGATGCTGTGTGGCTTGACACCTTTCCATAGCCAGGAAGTTTCTGATCTGTATGAGAATATCCTCTACAAACCTCTCT
GGATCCAAGGAAGCAAGACAGTAGCAGTCTGTGACCTCTTGCATGGCATTCTCCACAAGGTTTAGAAAAAAAGAATCTGT
GCCAAAGCAGACTTCTTGAGATAAAGTATCATATTTTCTACAACCCATGAACTGTGATGACATATTTCATAAGATACTCA
CTCTTCATTTCAACCCAAATGTGGTGGGG

Alignment

ORF - retro_mdom_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.49 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GELFFHLQREHC-FLEPRA-RFYAAEVASAI-GYLHSLNIIYRDLKPENILLDCQGHVVLTDFGLCKEGM
          G..FFHL..EHC.FL.......Y..EVA....G.LHSLNIIYRDLKPE.ILLDCQ.HVV.T.FGLCKE.M
Retrocopy GVEFFHLKCEHC<FLRTLSLNLYDTEVAGML<GSLHSLNIIYRDLKPEDILLDCQRHVVSTYFGLCKEEM

Parental  EPEETTSTFCGTPEYLAPEVLRKQPYDRTVDWWCL-GAVLYEMLCGLPPFYSRDVSEMYENILHKPLQIQ
          E.EE.TS..CG.P.Y.APE.LRKQPYD.T...WCL.GAVL.EMLCGL.PF.S..VS..YENIL.KPL.IQ
Retrocopy ELEEITSNLCGIPSYFAPEALRKQPYD*TLE*WCL<GAVL*EMLCGLTPFHSQEVSDLYENILYKPLWIQ

Parental  GGKTVAACDLLHGLLHKDQKKRLGAKADF-LEIKNHVFFS-PINWDDLYHKRLTPPFNPNVVG
          G.KTVA.CDLLHG.LHK..KKR..AKADF.LEIK.H.F...P.N.DD..HK.LT..FNPNVVG
Retrocopy GSKTVAVCDLLHGILHKV*KKRICAKADF<LEIKYHIFYN<PMNCDDIFHKILTLHFNPNVVG

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	16.81 RPM
SRP007412_cerebellum	0.00 RPM	11.75 RPM
SRP007412_heart	0.00 RPM	2.99 RPM
SRP007412_kidney	0.00 RPM	526.73 RPM
SRP007412_liver	0.00 RPM	360.50 RPM
SRP007412_testis	0.00 RPM	0.98 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1083 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1083 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000015157	1 retrocopy	retro_mmur_1287,
Monodelphis domestica	ENSMODG00000001260	1 retrocopy	retro_mdom_1083 ,
Monodelphis domestica	ENSMODG00000014313	2 retrocopies	retro_mdom_1502, retro_mdom_819,