RetrogeneDB ID: retro_mdom_1670

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:113314816..113315013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025763
• Aliases: None
• Description: None

Sequence

>retro_mdom_1670
GAACAAAACATCTTACTTAACCTATTAAAAGACTTCTACAAAAAGCAATATGCCCTGAAATTTTTAGGCCATTATGTGAT
CTTTATTAGGAGATGAGGAAATGCCTGAAAAAAGAATGTAAAGAAAAGAGGGCCAAGAGCAGGGCTTTTGGAGAAGCTGA
GCAACAGAAATTTACTAATGTTTGAGAAAAGCTAGAG

Alignment

ORF - retro_mdom_1670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.22 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECNILINLLKECHKKHNVLKF-FGHCNEIDREMRKCLKKEYGERRAKSRAIGEAKRQKLSGISEESE
          E.NIL.NLLK...KK...LKF.F........EMRKCLKKE..E.RAKSRA.GEA..QK.....E..E
Retrocopy EQNILLNLLKDFYKKQYALKF<FRPLCDLY*EMRKCLKKECKEKRAKSRAFGEAEQQKFTNV*EKLE

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	7.99 RPM
SRP007412_cerebellum	0.00 RPM	5.55 RPM
SRP007412_heart	0.00 RPM	17.14 RPM
SRP007412_kidney	0.00 RPM	3.95 RPM
SRP007412_liver	0.00 RPM	5.54 RPM
SRP007412_testis	0.00 RPM	28.68 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1670 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1670 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013929	2 retrocopies	retro_amel_397, retro_amel_681,
Bos taurus	ENSBTAG00000017009	1 retrocopy	retro_btau_109,
Echinops telfairi	ENSETEG00000010422	3 retrocopies	retro_etel_2190, retro_etel_357, retro_etel_816,
Felis catus	ENSFCAG00000004977	1 retrocopy	retro_fcat_193,
Loxodonta africana	ENSLAFG00000004378	2 retrocopies	retro_lafr_311, retro_lafr_896,
Microcebus murinus	ENSMICG00000011915	2 retrocopies	retro_mmur_1149, retro_mmur_701,
Monodelphis domestica	ENSMODG00000025763	1 retrocopy	retro_mdom_1670 ,
Sorex araneus	ENSSARG00000008906	2 retrocopies	retro_sara_712, retro_sara_84,
Sarcophilus harrisii	ENSSHAG00000001006	1 retrocopy	retro_shar_254,
Tupaia belangeri	ENSTBEG00000000038	3 retrocopies	retro_tbel_1840, retro_tbel_1979, retro_tbel_2249,