RetrogeneDB ID: retro_mdom_1393

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:271871135..271871536(-)
• Located in intron of: ENSMODG00000003818

Retrocopy information

• Ensembl ID: ENSMODG00000024253
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NABP1
• Ensembl ID: ENSMODG00000011862
• Aliases: None
• Description: nucleic acid binding protein 1 [Source:HGNC Symbol;Acc:26232]

Sequence

>retro_mdom_1393
CATGAGGTGAGGATCTGCAAAGTAGCAGACAAAACAGGTAGCATCAATATATCTATTTGGGATGATATTGACAACCTGAT
CCATCCTGGGGACATAATCCGACTCACCAGGGGGTATGCTTCAGTTTTAAAGGCTTTCTGACCCTCTACACTGACCATGG
GGGTGACTTACAGAAGATTGGAGAATTCTGTATGGTTTATTCTGAGGGCCCCAACTTCAGCAAGTCAGACCCTGAGTAGA
ATGCCCAGCAGCTCCCCAGCAAGATGGTACAGAACGAAAACACCTCTGCCACTTCCCAGCCTCCAGCTGGCCCTCCTGCA
GCCTCTCCAGCCTCTGAGAGTCAGAATGGGAATGGCCTAACCATTCCCCTCCCCACCCTGGCCCAGGCAGTGGTTCCCAT
T

Alignment

ORF - retro_mdom_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.15 %
• Parental protein coverage: 70.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HEVRSCKVADKTGSITISVWDEIGGLIQPGDIIRLTRGYASM-WKGCLTLYTGRGGELQKIGEFCMVYSE
          HEVR.CKVADKTGSI.IS.WD.I..LI.PGDIIRLTRGYAS...KG.LTLYT..GG.LQKIGEFCMVYSE
Retrocopy HEVRICKVADKTGSINISIWDDIDNLIHPGDIIRLTRGYASV<FKGFLTLYTDHGGDLQKIGEFCMVYSE

Parental  VPNFSEPNPDYLGQQ--NKVAHGEQKNNSSASNLGTGTFGPIGTGRANGRGPVNPQLPAAANVQPV
          .PNFS...P....QQ...K....E.....S....G.....P......NG.G...P....A..V.P.
Retrocopy GPNFSKSDPE*NAQQLPSKMVQNENTSATSQPPAGPPAASPASESQ-NGNGLTIPLPTLAQAVVPI

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_1393 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1393 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011862	1 retrocopy	retro_mdom_1393 ,
Oryctolagus cuniculus	ENSOCUG00000017546	2 retrocopies	retro_ocun_1146, retro_ocun_991,
Procavia capensis	ENSPCAG00000012746	1 retrocopy	retro_pcap_297,
Tupaia belangeri	ENSTBEG00000001158	1 retrocopy	retro_tbel_3393,