RetrogeneDB ID: retro_mdom_1517

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:94737276..94737767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020427
• Aliases: None
• Description: None

Sequence

>retro_mdom_1517
CTGTATTACCAGATATTAAACTTTGCCATGATTCTATTTTCTACTCTTATGATATGGGAAGGCTTGATAGTTGCCACTGG
AAGTGAAAGTCCTATTGTGGTGGTGCTGATTGGCAGTATAAAGCCAGCATTTTATAGAGGAGACCTTCTGTTTTTAACAA
ATTTCCAGAAAGATCCCATTAGAGCTAGGGAAATAGTCATTTTTTAAAGTTGAAGTAAGAGATATTCCTATAATCCACAG
AGTCTTCAAAGTTCACAAAACGATAATGGAAATGTCAAATTTTTGACTAAAGGAGATAATAATGAAATTGATGATAGAGG
TTTGTACAGAGAAATTCAAAACTGACTAGAAAAAAAAAGAATGTTGTAGGAAGAGCAAGAGGGTTTTTGCCATACATTGG
GATGGTTACCATAATCATGAATGATCATCTGAAATTCAAGTATGCTCTTTTGGCTATAATGGGTGCATATGTGATAATGA
AATGTGAATCC

Alignment

ORF - retro_mdom_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.25 %
• Parental protein coverage: 92.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LYYQILNFAMIVSSALMIWKGLIVATGSESPIVVVLSGSMEPAFHRGDLLFLTNFRKDPIRAGEIVV-FK
          LYYQILNFAMI..S.LMIW.GLIVATGSESPIVVVL.GS..PAF.RGDLLFLTNF.KDPIRA.EIV..FK
Retrocopy LYYQILNFAMILFSTLMIWEGLIVATGSESPIVVVLIGSIKPAFYRGDLLFLTNFQKDPIRAREIVI>FK

Parental  VEGRDIPIVHRVIKVH-EKDNGNVKFLTKGDNNEVDDRGLYKEGQNWLEKKDVV-GRARGFLPYIG-MVT
          VE.RDIPI.HRV.KVH...DNGNVKFLTKGDNNE.DDRGLY.E.QN.L...........GF....G.MVT
Retrocopy VEVRDIPIIHRVFKVH<QNDNGNVKFLTKGDNNEIDDRGLYREIQN*LXXXXML*EEQEGFCHTLG<MVT

Parental  IIMNDYPKFKYALLAVMGAYVILKRES
          IIMND..KFKYALLA.MGAYVI.K.ES
Retrocopy IIMNDHLKFKYALLAIMGAYVIMKCES

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_1517 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1517 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517 , retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,