RetrogeneDB ID: retro_mdom_41

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:23023486..23024173(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006985
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002508
• Aliases: None
• Description: None

Sequence

>retro_mdom_41
ACCAAGGGGACTCTAGTAGATCATTCCTACGTAGACACCCATATGCTCCTTCACCCAGAGCTGCTCTCTCGGGAGTTCCT
GCTGCTCACACTGCAGGAAAAAAATATAATTGGTAAAGAGGAAATAAAGACCAGCAAAAATGACCTTATTGCTCTCTATA
ACCGCCATGCATTGCCATTGCCTCAAAGGCAATTACCAAAAAGTAGATGGGGCAAAGTAGTTGAAGAGAAAAGAGAAGTG
AAAAATGAATTGAAAAATGAGCAAAAAAGTGATGTGAGTGTGGCAGCTTCAAGGAAAAGACCCCGCATAGTCTTTGATGG
CAATTCCACAAGTACGAGGATAAAAGTAAGAAGGACAGAAAAGGCAGCTAATGATGGCTCACAACCTCCTCCATCAGCTG
GCTTTACTAACAGTACCATTATCAAGTTACCAAATTCAAAAGCTTCCTCTGTACCTTCCACTTTGCCTACAGGCCTTAAA
GTGAACCCCCCAAATGACACTAAACAGAGCCCTGTGTTAATGGATAGTAGTACAGTGGCCAATGTAAAATCACAACCTTT
GTCTCATGTTGAGGAAACTTCTGTTGTGAAATTAAAGAGAATTGTTCCAAGAGAAGACGCAAAGTCAGTGAACGAATTCA
AGTCCTCAGGAACAAAGAAAAAGATCCAACGTATTACATGGCCATGA

Alignment

ORF - retro_mdom_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.01 %
• Parental protein coverage: 94.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEMLLHPELLSQEFLLLTLEQKNIVVEEEIKINKDDLTDFYVQHAIPLPQRELPKSRWGKMMEKKRG-QN
          ..MLLHPELLS.EFLLLTL..KNI...EEIK..K.DL...Y..HA.PLPQR.LPKSRWGK..E.KR...N
Retrocopy THMLLHPELLSREFLLLTLQEKNIIGKEEIKTSKNDLIALYNRHALPLPQRQLPKSRWGKVVEEKREVKN

Parental  ELKNEHKRNMSVESLRKRPLIVFDGNSTSTSIKVRKTENGTNDRLKPPPSVGVTNNTFRKLPHSNTSSLI
          ELKNE.K...SV...RKRP.IVFDGNSTST.IKVR.TE...ND...PPPS.G.TN.T..KLP.S..SS..
Retrocopy ELKNEQKSDVSVAASRKRPRIVFDGNSTSTRIKVRRTEKAANDGSQPPPSAGFTNSTIIKLPNSKASS--

Parental  LPSTLPTDIKVESNNDTKQNHVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEAESVSDCKPTEAK
          .PSTLPT..KV...NDTKQ..VLM.S.ST.ANVKS.PLS.V..T.VVKLKR..P.E.A.SV...K....K
Retrocopy VPSTLPTGLKVNPPNDTKQSPVLMDS-STVANVKSQPLSHVEETSVVKLKRIVPREDAKSVNEFKSSGTK

Parental  RKIQHVTWP
          .KIQ..TWP
Retrocopy KKIQRITWP

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_41 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_41 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002508	3 retrocopies	retro_mdom_1092, retro_mdom_1870, retro_mdom_41 ,