RetrogeneDB ID: retro_mdom_263

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:144654234..144655830(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025024
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012222
• Aliases: None
• Description: None

Sequence

>retro_mdom_263
ATGGTGGACGTGCTGAGCATCCTGTGCCAATATAATATCCAGAAAAAGGAGATCGTGGTGAAGGGGGACGAGGTGATCTT
CGGCGAGTTCTCCTGGCCCAAGAATGTCAAGACCAACTATGTGATTTGGGGGACAGGGAAGGAAGGGAAACCCATAGAAT
ACTACACTTTAGATTCCATTTTGTTCCTGCTTAATAATGTACATCTTTCTCATCCTGTATATGTCCGGCGTGCAGCTACT
AAAAACATTCCTGTGGTTAAAAGACCTGATAGAAAAGATTTGCTTGGATATCTAAATGGCGAAACCTCAACATGTGCAAG
TATTGACAGAAGTGCACCCCTTGAAAGAGGCCTTCCAAGATCCACACAAGTAAAAAGAGCAGCAGATGAAATATTAGTAC
AGGCAAAGAAATCACAAATTGAGGATGCAGAGTGTGTACGTCTTGATAAGGAGCGATTGGCTGCTCGCTTGGAGGGTCAC
AAAGAAGGGATTGTACAGATGGAGCAGATTAGATCCCTATCTGAAGCTATGTCTGTGGAAAAAATTGCTGCAATCAAAGC
CAAAATTATGACCAAGAAAAGGTCTACTATCAAGACTGATCTAGATGATGATATAACTGCACTTAAACAAAGAAGTTTTG
TTGATGCTGAAGTGGATGTGACCAGAGATATTGTGAGTCGAGAGAGAGTATGGAGGACAAGAACTACTATTCTGCAAAGC
ACAGGAACGAATTTTGCCAAGAATATTTTTGCATTTCTTCAGTCTGTAAAAGCCAAGGAGGAAGGGCGTGCCTCGGAGCA
GAGGTCTGCACCCAATACAGCACCTGTGGATCCCACATTACAGAATAAACCACCTATTCCAGCTGCCTATAACAGATATG
ATCAGGAAAGATTCAAAGGAAAAGAAGAAATGGAGGGCTTCAAAATTGATACAATGGGCACCTACCATGGAATGACTCTG
AAGTCTGTAACGGAGGGTGCATCAGCTCATAAGACTCAAACTCCAGCTGCACAGCCAGTGCCAAGACCAGTTTCTCAAGC
AAGACCTCCTCCAAACCAGAAAAAAGGATCTCGAATACCCATTATCATTATTCCAGCAGCTACCACATCTTTAATAACTA
TGCTTAATGCAAAAGATCTTCTCCAAGACCTAAAATTTGTTCCATCAGATGAGAAGAAAAAACAAGGCTGCCAGAGAGAA
AATGAAATACTCATCCAGAGATGGAAAGATCAGATGCAGCCAGGGGGCACTGCTATACGTGTGATAGTCCCCTATCGAGT
AGTAGATCAGCCCCTCAAACTTATGCCTCAAGACTGGGATCGTGTTGTGGCAGTTTTTGTACAGGGCCGTGCATGGCAGT
TCAAAGGTTGGCCATGGCTATTACCTGATGGATCACCAGTTGACATATTTGCTAAAATTAAAGCCTTTCATCTAAAGTAT
GATGAAGTACACCTAGATCCAAATGTACAGAAATGGGATGTAACAGTATTAGAATTAAGCTACCACAAACGTCACTTGGA
CAGACCAGTGTTTTTGCATTTTTGGGAAACATTGGACAGGTACATGGTGAAGCATAAATCCCATTTGAGATTCTGA

Alignment

ORF - retro_mdom_263 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.88 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVIWGTGKEGQPREYYTLDSILFLLNNVHLS
          M.DVLS.L.QYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVIWGTGKEG.P.EYYTLDSILFLLNNVHLS
Retrocopy MVDVLSILCQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVIWGTGKEGKPIEYYTLDSILFLLNNVHLS

Parental  HPVYVRRAATENIPVVRRPDRKDLLAYLNGETSTSASIDRSAPLEIGLQRSTQVKRAADEILAEAKKPRI
          HPVYVRRAAT.NIPVV.RPDRKDLL.YLNGETST.ASIDRSAPLE.GL.RSTQVKRAADEIL..AKK..I
Retrocopy HPVYVRRAATKNIPVVKRPDRKDLLGYLNGETSTCASIDRSAPLERGLPRSTQVKRAADEILVQAKKSQI

Parental  EDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQ
          ED.ECVRLDKERLAARLEGHKEGIVQ.EQIRSLSEAMSVEKIAAIKAKIM.KKRSTIKTDLDDDITALKQ
Retrocopy EDAECVRLDKERLAARLEGHKEGIVQMEQIRSLSEAMSVEKIAAIKAKIMTKKRSTIKTDLDDDITALKQ

Parental  RSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFAKNIFAILQSVKAREEGRAPEQRPAPNTAPVDPTL
          RSFVDAEVDVTRDIVSRERVWRTRTTILQSTG.NFAKNIFA.LQSVKA.EEGRA.EQR.APNTAPVDPTL
Retrocopy RSFVDAEVDVTRDIVSRERVWRTRTTILQSTGTNFAKNIFAFLQSVKAKEEGRASEQRSAPNTAPVDPTL

Parental  RNKPPIPAAYNRYDQERFKGKEGQNPF
          .NKPPIPAAYNRYDQERFKGKE....F
Retrocopy QNKPPIPAAYNRYDQERFKGKEEMEGF

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_263 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_263 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008675	2 retrocopies	retro_chof_2535, retro_chof_747,
Myotis lucifugus	ENSMLUG00000012093	2 retrocopies	retro_mluc_1439, retro_mluc_2152,
Monodelphis domestica	ENSMODG00000012222	1 retrocopy	retro_mdom_263 ,
Nomascus leucogenys	ENSNLEG00000018050	1 retrocopy	retro_nleu_2818,
Oryctolagus cuniculus	ENSOCUG00000016332	1 retrocopy	retro_ocun_302,
Otolemur garnettii	ENSOGAG00000000351	1 retrocopy	retro_ogar_767,