RetrogeneDB ID: retro_mdom_1994

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:24520181..24520943(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000007195
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006193
• Aliases: None
• Description: None

Sequence

>retro_mdom_1994
ATGAAGCCAGAAACATCTCGTATGTTCATTCTGAGTTCCCTTTGTTTAGCTTTTTATTGTTTGTGTACTGCTGACAAATT
CTACAATAGTGGCAACCATGAGTGGAAAAAGTTGATTATGGTTCATCTCTGGCCTACAACTGTGTGTAAGGAAATTGAAA
ATGACTGCAGAGAGCCCTCTAATTACTGGACAATCCATGGACTCTGGCCTGATAAAGTTTCAGAGTGTAACAGATCATGG
AACTTTGATTTAGATGAGATCAAGTATCTTTTGCCTGACATGAAACATTTCTGGCCTGATGTAATCCATCCATCTCCTAA
TCGAAGCCAGTTCTGGAAGCATGAGTGGGAGAAACATGGAACCTGTGCAGCCCAGTTGGACTCTCTAAATTCTCAAAAAA
ATACTTCAGTAAATGTCTGGAGTTTTATAAAGATATTGACCTCAATAGTATACTCCTGAAGTTGGGGATAGAGCCAGCAA
TTTCATAATACCAAATTGAAGACATTAAGAATGCCCTTGTAAGTGTATATGGAGTAATACCCAAAATGCAGTGCCTGCCA
CCAGAAAAGGAAGAAGTACAAAAACTTGGTCAAATTGAATTCTGTTTCACCAAATATCTACAGTTGATAAATTTAATGAC
CCAAAGGTATATGCTCCCTTCCTGCAAGATGCATTGTTGACTGATGAGACTCCCAGAGTCTTGGGCTCTCTGTCTATGAA
AAAGGCCCAGTTTTCTATCCCCCTCCAGAAAAGACCCACCTT

Alignment

ORF - retro_mdom_1994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKPETSRMFILSSLCLAFYCLCTADKFYNSGNHEWKKLIMVHHWPTTVCKEIENDCRDPPNYWTIHGLWP
          MKPETSRMFILSSLCLAFYCLCTADKFYNSGNHEWKKLIMVH.WPTTVCKEIENDCR.P.NYWTIHGLWP
Retrocopy MKPETSRMFILSSLCLAFYCLCTADKFYNSGNHEWKKLIMVHLWPTTVCKEIENDCREPSNYWTIHGLWP

Parental  DKASECNRSWHFDLDEIKDLLPDMKHFWPDVIHPSPNRSQFWKHEWEKHGTCAAQLDSLNSQK-KYFSKC
          DK.SECNRSW.FDLDEIK.LLPDMKHFWPDVIHPSPNRSQFWKHEWEKHGTCAAQLDSLNSQK.KYFSKC
Retrocopy DKVSECNRSWNFDLDEIKYLLPDMKHFWPDVIHPSPNRSQFWKHEWEKHGTCAAQLDSLNSQK<KYFSKC

Parental  LEFYKDIDLNSILLKLGIEPEISYYQIEDIKNALVSVYGVEPKLQCLPPEEEEEIQILGQIEFCFTKDLQ
          LEFYKDIDLNSILLKLGIEP.IS.YQIEDIKNALVSVYGV.PK.QCLPP.E.EE.Q.LGQIEFCFTK.LQ
Retrocopy LEFYKDIDLNSILLKLGIEPAIS*YQIEDIKNALVSVYGVIPKMQCLPP-EKEEVQKLGQIEFCFTKYLQ

Parental  LINC-TDPKVYAPFLQDALLTDETP-MSLGLYVCKDGPVFYPPPEKTHL
          LIN...DPKVYAPFLQDALLTDETP..SLGL.V...GPVFYPPPEKTHL
Retrocopy LINL<NDPKVYAPFLQDALLTDETP<QSLGLSVYEKGPVFYPPPEKTHL

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_1994 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1994 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994 ,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529,