RetrogeneDB ID: retro_mdom_790

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:506208449..506208721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM18
• Ensembl ID: ENSMODG00000014284
• Aliases: None
• Description: transmembrane protein 18 [Source:HGNC Symbol;Acc:25257]

Sequence

>retro_mdom_790
CACATTGACTTGTCTGAGCCATGGTTACTGGGACTTTTATTCTTCCACATACTTTGCCTGTTGCTCACTTACCTTACTTT
CCAATGATATTGACTTCAGATTGAGCATTTCCTGTGTTTGGTGATTTTAGCTTATTCTGCTGAATACATTAATGAGCTAC
TGCTATGAATTGAAGGTCCTTTTCTAAACAATATTTTAATTCAAGAGGAATGTTTATTTCCATGGGGTTTTTTTCAGTTC
CATTGCTGTTAAATGCTATGATCATTGTGATT

Alignment

ORF - retro_mdom_790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 83.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HTDWSEPWLLGLLVFHILCLLLTYLTFQRYRLQIGHFMCLVILVYSAEYINEL-AAMNWRLFSKYQYFDS
          H.D.SEPWLLGLL.FHILCLLLTYLTFQ.Y.LQI.HF.CLVIL.YSAEYINEL..AMN.R.FSK.QYF.S
Retrocopy HIDLSEPWLLGLLFFHILCLLLTYLTFQ*Y*LQIEHFLCLVILAYSAEYINEL<TAMN*RSFSK-QYFNS

Parental  RGMFISM-VFSAPLLLNAMIIVV
          RGMFISM..FS.PLLLNAMIIV.
Retrocopy RGMFISMGFFSVPLLLNAMIIVI

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	5.13 RPM
SRP007412_cerebellum	0.00 RPM	5.88 RPM
SRP007412_heart	0.00 RPM	6.78 RPM
SRP007412_kidney	0.00 RPM	6.58 RPM
SRP007412_liver	0.00 RPM	10.07 RPM
SRP007412_testis	0.00 RPM	9.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_790 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_790 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000543	1 retrocopy	retro_chof_31,
Cavia porcellus	ENSCPOG00000012522	1 retrocopy	retro_cpor_1298,
Dipodomys ordii	ENSDORG00000001854	1 retrocopy	retro_dord_416,
Equus caballus	ENSECAG00000008640	1 retrocopy	retro_ecab_596,
Monodelphis domestica	ENSMODG00000014284	1 retrocopy	retro_mdom_790 ,