RetrogeneDB ID: retro_mdom_602

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:485352177..485352990(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000016530
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005468
• Aliases: None
• Description: None

Sequence

>retro_mdom_602
AGGTGTGCCACAATGGATGCTCTCTCTGAAGCAAAAAATGACTTTGCCTTTGGATGTTTTAAAAAAGAATCGGTGATGAA
AATAGCTCAAAGAATGTGTTATATTCTCCTCTGAGCCTCTACTGTGCCCTGTCTATGGTCTTAGATGGGGCCCAGGGAAA
TACTGCTGAACAGATACAACAGGTTCTTTCTTTTAAAAAAAGATACAGATATCAACCAACGTTTTCAGTCCTTTCTTGGA
GAAATTAATAAATCTGGTTCTTGGTGTCTACTAAGAATTGCCAACCAACTCTTTGGAGAAAAGACTTATGATTTCCATTC
ATCTTTTAAGGATTGTTGTCAGAAATTCTACCATTCAAATATGAAAGAACTTGACTTTGTTCATGATTTTGAAGCAGCAA
GAAAACACATCAATAAGTGGGTAGAAGAAAAAACAGAAGGTAAGATTGCAGAACTTCTGCCTAAAGATTCCATTTCTCCA
GTGACCTGTCTGGTACTTACAAATGCTATCTACTTCAGTGGAAAATGGAAAAAAAAACAATTTAACAAAGAAAAGACCAC
TGAAAAGATGTTCAAAATCAGCAAGGAGGAGCAAAAACTAGTACCAATGATGTATCAGAGATCTACATTTCATATGACTT
ATGTAGGAGAAGTGTTTACCAAGATCCTAGTTCTGCCTTACACTAGAGGACAAATGAGCATGGCCATTTTACTTCCGGAC
AAGAACAGGGATATAAAAATGTTGGAAGAAGCACTTACTTCTGACAAATTAGCAGATTGGCTAAATCTAGACATGATGGA
CCAAACTGAGGTC

Alignment

ORF - retro_mdom_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRATMDAFSEANNAFA-LDVFKK-VCEENSSKNVFYSPLSLYCALSMVLDGAKGNTAAQIQQVLS-LKKD
          R.ATMDA.SEA.N.FA.LDV.KK....ENSSKNV.YSPLSLYCALSMVLDGA.GNTA.QIQQVLS.LKKD
Retrocopy RCATMDALSEAKNDFA>LDVLKK>IGDENSSKNVLYSPLSLYCALSMVLDGAQGNTAEQIQQVLS>LKKD

Parental  TDIHQSFQSFLGEVNKSGSQCLLRIANQLFGEKTYNFHSSFKDCCQKFYHSNMEELDFAHDFEAARKHIN
          TDI.Q.FQSFLGE.NKSGS.CLLRIANQLFGEKTY.FHSSFKDCCQKFYHSNM.ELDF.HDFEAARKHIN
Retrocopy TDINQRFQSFLGEINKSGSWCLLRIANQLFGEKTYDFHSSFKDCCQKFYHSNMKELDFVHDFEAARKHIN

Parental  KWVEEKTEGKIVDLLPKDTISPMTCLVLTNAIYFGGKW-EKQFNKEKTTEKMFKISKEEQKLVPMMYQKS
          KWVEEKTEGKI..LLPKD.ISP.TCLVLTNAIYF.GKW...QFNKEKTTEKMFKISKEEQKLVPMMYQ.S
Retrocopy KWVEEKTEGKIAELLPKDSISPVTCLVLTNAIYFSGKWXXXQFNKEKTTEKMFKISKEEQKLVPMMYQRS

Parental  TFHMTYIGEVFTKILVLPYTGGQMSMAILLPDENRDIKMLEEALTSEKLADWLNLDMMDQTEV
          TFHMTY.GEVFTKILVLPYT.GQMSMAILLPD.NRDIKMLEEALTS.KLADWLNLDMMDQTEV
Retrocopy TFHMTYVGEVFTKILVLPYTRGQMSMAILLPDKNRDIKMLEEALTSDKLADWLNLDMMDQTEV

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_602 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_602 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017483	1 retrocopy	retro_btau_827,
Echinops telfairi	ENSETEG00000012630	1 retrocopy	retro_etel_1134,
Microcebus murinus	ENSMICG00000001981	1 retrocopy	retro_mmur_403,
Myotis lucifugus	ENSMLUG00000008803	1 retrocopy	retro_mluc_1610,
Monodelphis domestica	ENSMODG00000005468	2 retrocopies	retro_mdom_510, retro_mdom_602 ,
Mustela putorius furo	ENSMPUG00000000448	1 retrocopy	retro_mputfur_1037,
Mus musculus	ENSMUSG00000060147	2 retrocopies	retro_mmus_3191, retro_mmus_3192,
Pteropus vampyrus	ENSPVAG00000010001	1 retrocopy	retro_pvam_1243,
Tursiops truncatus	ENSTTRG00000003879	2 retrocopies	retro_ttru_1224, retro_ttru_1837,