RetrogeneDB ID: retro_mdom_1468

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:192151119..192151520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010850
• Aliases: None
• Description: None

Sequence

>retro_mdom_1468
AAATATTTCCTTAATGTAATGATAAATTGTGAAATACACTGTCCCCTCTATTGTGGAAATGTAACTAGAAGAGAGCAAGC
ATATCCTGAATGAACTTTAGATAGTGAAAATGTCATAAGGAAGTTTTCAGGTAGCTACAGATACTCTTCAAAACAGAACA
CATTTTATCACATAAGAAATCATTACAAAATTTTAAGAAGCATCAGGATGAGTATGGTTTATATTCCATCAATCCAAACT
TTCAGATCTCTCAAGAATCAGTAGGGAAGAGTAATATGAATGAGATATCTACATCTGATAACACAGAGATCTATCAAGAA
GTTGTAAATTATCTTGGGCATTCCACATTTAAGAGTCTCTTGTGCCAAGAAGCAAACTTTACAAGACAATGTTTATTGGA
T

Alignment

ORF - retro_mdom_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 54.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KCFLTAMRESGIHCPLCRGNVTRRERACPERALDIENVMRKFSGSCRCCAKQIKFYRMRHHYK-SCKKYQ
          K.FL..M....IHCPL..GNVTRRE.A.PE..LD.ENV.RKFSGS.R...KQ..FY..R.HYK...KK.Q
Retrocopy KYFLNVMINCEIHCPLYCGNVTRREQAYPE*TLDSENVIRKFSGSYRYSSKQNTFYHIRNHYK<NFKKHQ

Parental  DEYGVSSIIPNFQISQDSVGNSNRSETSTSDNTETYQGDASSTGHPTFKCPLCQEANFTRQRLLD
          DEYG..SI.PNFQISQ.SVG.SN..E.STSDNTE.YQ......GH.TFK..LCQEANFTRQ.LLD
Retrocopy DEYGLYSINPNFQISQESVGKSNMNEISTSDNTEIYQEVVNYLGHSTFKSLLCQEANFTRQCLLD

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_1468 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1468 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Erinaceus europaeus	ENSEEUG00000009856	1 retrocopy	retro_eeur_430,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468 , retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Mus musculus	ENSMUSG00000024317	2 retrocopies	retro_mmus_3726, retro_mmus_494,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Ochotona princeps	ENSOPRG00000011494	1 retrocopy	retro_opri_554,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,