RetrogeneDB ID: retro_mdom_1687

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:203752665..203753177(-)
• Located in intron of: ENSMODG00000012312

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1E2
• Ensembl ID: ENSMODG00000018481
• Aliases: None
• Description: aldo-keto reductase family 1, member E2 [Source:HGNC Symbol;Acc:23437]

Sequence

>retro_mdom_1687
ACAGACTACATGGACACATGGGAGGCTATAAAGGATCTATTGAATGAGGGACTGGTGAAAGCTATTGGAGTTTCAAACTT
CAACCACCAACACATTGAGAGACTTCTGAACAAGCCTAGTTTATGATACAAGCCCACAAACAACCAGATAGAGAGCCACC
CATTTTGTACTCAGAAGCTGATCAACTATTACCATTCAAAAGGTATCACTGTGAGAGCCTATCATCCACTTGGGGGCACA
AGTAATGCTCGGATGAACCCATTATTAAGAAGATTACAGAAAAATACAAGAAATCTGAAGCTCAGGTTTTGATCCACTTT
CAGTTACAACAAAACGTGGCAGTAATCCCTAAGTCTGTCACCCCAAGTCGAATAAAAGAGAACTTTGAGGTGTTCAATTT
TGAACTCACAAAAGAAGAAATGGATGCCATCCTGAGCCTGAATAGGAATTTTCGATTGGCTGAATTAGCTTTTTCTAAAA
ATCACAAAGACTATCCTTTCAACATTGAATAC

Alignment

ORF - retro_mdom_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 57.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TDYLDTWEAMEDLLSEGLVKAIGVSNFNHQQIERLLNKPGLRYKPTNNQIESHPFCTQEKLINYCRSKGI
          TDY.DTWEA..DLL.EGLVKAIGVSNFNHQ.IERLLNKP.L.YKPTNNQIESHPFCTQ.KLINY..SKGI
Retrocopy TDYMDTWEAIKDLLNEGLVKAIGVSNFNHQHIERLLNKPSL*YKPTNNQIESHPFCTQ-KLINYYHSKGI

Parental  SVTVYRPLGGTSNVL-DEPVIKKIAEKYKKTEAQVLIRFQLQRNVAVIPKSVTPSRIKENFEVFDFELTK
          .V..Y.PLGGTSN...DEP.IKKI.EKYKK.EAQVLI.FQLQ.NVAVIPKSVTPSRIKENFEVF.FELTK
Retrocopy TVRAYHPLGGTSNAR<DEPIIKKITEKYKKSEAQVLIHFQLQQNVAVIPKSVTPSRIKENFEVFNFELTK

Parental  EEMDAILSLNRNFRLAGLAFSKNHKDYPFNIEY
          EEMDAILSLNRNFRLA.LAFSKNHKDYPFNIEY
Retrocopy EEMDAILSLNRNFRLAELAFSKNHKDYPFNIEY

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_1687 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1687 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018481	1 retrocopy	retro_mdom_1687 ,
Mustela putorius furo	ENSMPUG00000016247	1 retrocopy	retro_mputfur_65,
Rattus norvegicus	ENSRNOG00000017165	1 retrocopy	retro_rnor_1441,