RetrogeneDB ID: retro_mdom_1475

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:217385406..217385765(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020810
• Aliases: None
• Description: None

Sequence

>retro_mdom_1475
CATCCCCCCGCAGGCCGACGAAACAGCCTCACAGCCAGCGATTCTGAAGGCAACTTCCGGAAATCGAGCCAGGGGGAGAG
TGTGGCCTCGTGGTCCGACCCTTCCATTCCAGTTCCAGTGAGGCATATTCAGTTTAACCCAGGGAACGCTCATAGAACCA
ACATCTGCCCAGGACTAAAGCCTCTGATCACCAGACAAAGACAAGAAAAGCCAATCCTCCACGTTCAGAGATGACAAACT
CTACAGAAGCACAGAAGCTCCAAAATACCAAGAAAAATAAGAAGAAAGGGGCGACTCTGCGACACATTCTATCGAGCCAA
AATATAAAATACAGAGCAGATAGAGAGATATACAGAAAA

Alignment

ORF - retro_mdom_1475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 58.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HHPYGQRNSLRASYSEGNFRKATRPREPGESVAPWSDPSTPVPVRHTQFNPGKPHKTN-NLPRTKASEHQ
          H.P.G.RNSL.AS.SEGNFRK.......GESVA.WSDPS.PVPVRH.QFNPG..H.TN..LPRTKAS.HQ
Retrocopy HPPAGRRNSLTASDSEGNFRKSSQ----GESVASWSDPSIPVPVRHIQFNPGNAHRTN<HLPRTKASDHQ

Parental  TEIRKANPPHSEMANSTEAQKPQNNKKNKKKGVQDSIARIQVSDQRTSYKVSQGINSK
          T..RKANPP.SEM.NSTEAQK.QN.KKNKKKG......R...S.Q...Y.....I..K
Retrocopy TKTRKANPPRSEMTNSTEAQKLQNTKKNKKKG---ATLRHILSSQNIKYRADREIYRK

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_1475 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1475 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000020810	2 retrocopies	retro_mdom_1475 , retro_mdom_1921,