RetrogeneDB ID: retro_mdom_880

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:271131644..271132272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNB2
• Ensembl ID: ENSMODG00000004610
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), beta polypeptide 2 [Source:HGNC Symbol;Acc:4398]

Sequence

>retro_mdom_880
AAGAGGCCAAGGGGCAAAGTCAGGATCAACAGAGAGCTGCCAGGCCACACTGGGTATCCGTCTTGCTGTAGATTTTTAGA
TGACAACTAGATCATCATTAGCTATAGTGACACAGCCTGTGCCTTATATGATATAGAAATAGGACAGCAAACATTGAGCT
TTTTGGGGCACAGTGGGGAGTTAATGTTCCTGTTCCTGGCTGCAGATGGCCAGAGCATATAAATTCATCTCTGGTGCCTG
GAATGCTTCTATCAAAATTGTGATACGTTTGGGACGCTCTATGCCAAACAAACTTTTCCAGGCCATGAGTCTTATATCAG
TGCTGTGGACTTCTTTCCAAGTGATATGCCTTCACCAGGATCTCAGCTGATACTACATGCCACTTCTTTGACCTTTGGGA
TGACCAGGAGTGATATATGTACTCTCCTGACAATTTAATCTGTGGTTTCATCTCTTCTATCTCTGAAGGTGGACAGTTAC
TACTGAATGATTGTGATGACTTCAACTATAATATTTGGATGCCATGAAAGGAAGCTGGGCAGGTGTCCTTGATGGCCATG
ACAATTTTTGCTGTCTTGTGATGACCATTGATGGGGTGGCTATGACCACAGTTCTGTGGGACTTCTTT

Alignment

ORF - retro_mdom_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 61.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KTREGNVRVSRELPGHTGYLSCCRFLDDNQIITSSGDTTCALWDIETGQQTVG-FAGHSGDVMSLSLAPD
          K...G.VR..RELPGHTGY.SCCRFLDDN.II.S..DT.CAL.DIE.GQQT...F.G..G...S.S....
Retrocopy KRPRGKVRINRELPGHTGYPSCCRFLDDN*IIISYSDTACALYDIEIGQQTLS>FWGTVGS*CSCSWLQM

Parental  GRS--FVSGACDASIK-LWDVRDSMC-RQTFTGHESDINAVAFFPNG-YAFTTGSDDATCRLFDLRADQE
          .R...F.SGA..ASIK.L..V.D..C..QTF.GHES.I.AV.FFP...YAFT..S.D.TC..FDL..DQE
Retrocopy ARAYKFISGAWNASIK>L*YVWDALC>KQTFPGHESYISAVDFFPSD<YAFTRISADTTCHFFDLWDDQE

Parental  LLMYSHDNIICGITSVAFSRSGRLLLAGYDDFNCNIW-DAMKGDRAGVLAGHDNRVSCLGVTDDGMAVAT
          ..MYS.DN.ICG..S...S..G.LLL...DDFN.NIW.DAMKG..AGVL.GHDN...CL..T.DG.A..T
Retrocopy *YMYSPDNLICGFIS-SISEGGQLLLNDCDDFNYNIW<DAMKGSWAGVLDGHDN-FCCLVMTIDGVAMTT

Parental  GSWDSF
          ..WD.F
Retrocopy VLWDFF

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_880 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_880 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015074	1 retrocopy	retro_cjac_1727,
Macropus eugenii	ENSMEUG00000003863	1 retrocopy	retro_meug_1275,
Monodelphis domestica	ENSMODG00000004610	1 retrocopy	retro_mdom_880 ,