RetrogeneDB ID: retro_mdom_1927

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:178881726..178882047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013617
• Aliases: None
• Description: None

Sequence

>retro_mdom_1927
ATGAATGCACCTCTGGTCTTCAAGTCTTTCCTTCTCTTTGAGGGAGAGAAGAAGATTGCTATCAACAAGCACACCAAGGT
ACCCAGTGCTTGTTTGTTCACCATCAACAAAGAGGATCACATACTGGGAAACATCATCAAATCACAGTTATTGGAAGCCC
CCCAGATGCTATTTGCAGGCTATAAAGTCCCTGACCCACTGGAACATAAGACTGTCATTCCTATACAGACCACTCCAGAT
TACCACTCTCAGGAGACTTTTATGAATGCTATCCCAGATCTGATCAGCTAGTTCTCCTTGTTGGAAGAGTGATTTCAGAT
T

Alignment

ORF - retro_mdom_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 83.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHK
          MNAP..F.SFLLFEGEKKI.INK.TKVP.ACLFTINKEDH.LGNIIKSQLL..PQ.LFAGYKVP.PLEHK
Retrocopy MNAPLVFKSFLLFEGEKKIAINKHTKVPSACLFTINKEDHILGNIIKSQLLEAPQMLFAGYKVPDPLEHK

Parental  IIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRV
          ..I..QTTPDY..QE.F.NAI.DLIS..SLLEE.F..
Retrocopy TVIPIQTTPDYHSQETFMNAIPDLIS*FSLLEE*FQI

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_1927 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1927 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013617	2 retrocopies	retro_mdom_1699, retro_mdom_1927 ,
Sus scrofa	ENSSSCG00000024080	1 retrocopy	retro_sscr_53,