RetrogeneDB ID: retro_mdom_1343

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:83933723..83934251(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEX9
• Ensembl ID: ENSMODG00000008144
• Aliases: None
• Description: testis expressed 9 [Source:HGNC Symbol;Acc:29585]

Sequence

>retro_mdom_1343
AAGATCAATAAATCTGATTCCATAACGAAAATTCAAAACAAGTCACAGTCTGGGAATAAAAGAAAGAGAAAAACTTGAAG
TATAAAATTGAAACGTGTTAATTGCAAACTACCAATGATGTTGCCACCCAGAGGACTTCATAGACTTTTCACTTACAAAT
ACAATTAATAGAATTGAAGGAAAATTAGAGCGATTTACCTGATGACACAGATGATGATGATATTTTCTCTGGGCTCAAGG
AAGACATTGAAACTGAGGACCAGATCAGATTTCTAAAGGCAAAACTCCATGTTATATAGGTGGAATTGGATAGACTTATG
TATGATTGTAATAAAAAAGGAGGATGAAGTAAGGCATTTAAAAACATCTCTTAAAAGATATTAATGAATTTTATATTAGA
ATGGAGAAAATAATATTCAACAATCTCAGATTGAAAAATACAAAAATATTTTCAGAAGAATCAATCAAAAATGTGATAGA
TTTCAGCAACAGCTGATTGCAGTAGAAAAGAAATTGGATACTAGAAAG

Alignment

ORF - retro_mdom_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.3 %
• Parental protein coverage: 62.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KIKKSDSITDLQNKPKSGNKGKKKTSSVKLKHAN-MQLSTDVAV-PEDFTD-FSLKSTIHRIEGKLDEGD
          KI.KSDSIT..QNK..SGNK.K.KT.S.KLK..N..Q...DVA..PEDF.D.F.L...I..IE.K....D
Retrocopy KINKSDSITKIQNKSQSGNKRKRKT*SIKLKRVN<LQTTNDVAT<PEDFID>FHLQ--IQLIELKEN*SD

Parental  LLVDIDED-VFHGLSEGIVTEAQIRFLKAKLRVMQEELDSLVYDCN-KKEDETRNLKAS-LKDINEERVR
          L..D.D.D..F.GL.E.I.TE.QIRFLKAKL.V...ELD.L.YDCN.KKEDE.R.LK.S.LKDINE...R
Retrocopy LPDDTDDDDIFSGLKEDIETEDQIRFLKAKLHVI*VELDRLMYDCN>KKEDEVRHLKTS>LKDINEFYIR

Parental  MERTINIQQSQIEKYKMLSEE-LNKKCDGLQQQLTAVEKELDNRR
          ME..I..........K..SEE..N.KCD..QQQL.AVEK.LD.R.
Retrocopy MEKII-FNNLRLKNTKIFSEE<INQKCDRFQQQLIAVEKKLDTRK

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	30.16 RPM
SRP007412_cerebellum	0.00 RPM	9.79 RPM
SRP007412_heart	0.00 RPM	1.20 RPM
SRP007412_kidney	0.00 RPM	5.27 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	283.85 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1343 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1343 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000008144	1 retrocopy	retro_mdom_1343 ,