RetrogeneDB ID: retro_mdom_648

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:674095152..674095854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008042
• Aliases: None
• Description: None

Sequence

>retro_mdom_648
ATGGCTCATGGGCTTTGGAAGGGTAATTATCTGTTCAATGTCTTCATGGATGCTAAGCACCACAAGCACAAGCCTAGTCA
AGAAGATGCTCTTCATCAAGTGTAGTCCATGGAAAAAAGAGCTTGCTGCACAGCAAACATCACCATTGCAGTCCATGAGA
ATCCCTCCCACTTGTATAAGTTCAACTTTAACCACTGTGGGACAATGACTCCAGCCTGCAAACACCACTTTGTCCAGGAC
CTGTGTCTCTACGAGTGTTCCCCAAACCTGGGACCCTGGATCCAGCCTGTAAATTCAAGCTGGAGGAAGTAACGAGTCTT
GAATATTCCCCTCTGCAAAGAGGACTGTAACATGTTGTGGGAGGACTATAAAGCCTCCTATTCCTGAAAAGAGAACTGGC
ACAAAGGCTGGAATTGGTCTTCAGGGATTAACAAGTGTCCAGTTAAGGCTGCTTGAGATCCTTTCTCCTTTTACTTCCCA
ACACCAGCCTCCATCTGGGAGAATATTTGGAGTCACTCTTATAATGCAAGCTCTTATGGCGGAGCCAGTGGCAAATGTAT
CCAGATGTGCTTTGACCTAGCCCAGGGAAACCCCAATGAAGCTGTGGCTAAATACTATGCTTATAGCTCTGCCCCAGGCA
TCTCCAGTTGGAGGGCCAGTTTTTCCTTCTTGACTCTGATGCTGCTGCTGCTTCTCTGGGCT

Alignment

ORF - retro_mdom_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 91.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHGLQKGDDLLNVCMDGKHHKYKPGQEDNLHQQCSPWKKRACCTASTSIAAHEDASHLYKFNFSHCGML
          MAHGL.KG..L.NV.MD.KHHK.KP.QED.LHQ..S...KRACCTA...IA.HE..SHLYKFNF.HCG..
Retrocopy MAHGLWKGNYLFNVFMDAKHHKHKPSQEDALHQV*S-MEKRACCTANITIAVHENPSHLYKFNFNHCGTM

Parental  TPACKRHFVQDLCLYECSPNLGPWIQPVNSSWRKERVMNIPLCKEDCNMWWEDCKTSYTCKENWHKGWNW
          TPACK.HFVQDLCLYECSPNLGPWIQPVNSSWRK.RV.NIPLCKEDCNM.WED.K.SY..KENWHKGWNW
Retrocopy TPACKHHFVQDLCLYECSPNLGPWIQPVNSSWRK*RVLNIPLCKEDCNMLWEDYKASYS*KENWHKGWNW

Parental  SSGINECPVKAACHPFSFYFPTPTSLCENIWSRSYNASHSYGRGSGKCIQMWFDPAQGNPNEAVAKFYAN
          SSGIN.CPVKAA..PFSFYFPTP.S..ENIWS.SYNAS.SYG..SGKCIQM.FD.AQGNPNEAVAK.YA.
Retrocopy SSGINKCPVKAA*DPFSFYFPTPASIWENIWSHSYNAS-SYGGASGKCIQMCFDLAQGNPNEAVAKYYAY

Parental  SAAPDIFSWGCSFPFLTLLLLLLLWA
          S.AP.I.SW..SF.FLTL.LLLLLWA
Retrocopy SSAPGISSWRASFSFLTLMLLLLLWA

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_648 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_648 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648 ,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,