RetrogeneDB ID: retro_mdom_1825

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:12658084..12659063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010049
• Aliases: None
• Description: None

Sequence

>retro_mdom_1825
CCTTTCAGCACAGGGTCAATAACATTCAAGGAAGTGGTTGTGAACTTCCCCCAAGAGGAGTGGTGCCTGTTGGATCATTC
TCAGAAAGAGCTGTATAGGGAGATCATGCTGGAGAATGTGCAGAATCTACTCTCTATGGAGCTTCTAGTTCATAGAGAAG
ATTTTATCGCCTGTTTTCAACAAAGGGAATCACCATGGCTGGTAGAGCATAAAGGCCCAAAGAACTCCTGTCCAGAGGCA
GAGATTAATTTTAAAGTGAAGGAGATGTCTGCAAAGCTAAGCCTTTTTGTGGAATGATTTGGCCCCCAAAGACGCATGAA
TCAGGATCCCTGTGATTTTATTTTGAGACAAATGTATGTCTCTAATATCAAGGTAAATAAAAATTCAAAGAGTGACTGTG
AATTCGAAAAACTGCAGAGAAATTCAGCCAATATTCAGTTCTAAATCAGTATATAAAATTGAATTCAAGAAATGACTGTT
GTCAGGATAGTGAATTCAGCAAATGCTTTCCTGAATAAGTAGGATTTATTCAGTCACCTAAGAAACCTCCTGAAATGCCC
ACGTATCAAGATAACCTGGGGGAATGGCCTTTGGTTAAAGTTTAGGCCTCATTAGACATCCAAAAAGTAAATGTGTAGAG
ATGCTTTCTGTGAGTAATAAAGGTGGGAAACCTTTCAGTCAGAACTCTGAGCTTGGTTTACATCAAATAGTCCACAATGG
AGAGAAACCTTATGAATGTAAACACTGTGGAAAGGCTTTCACAGTGATGGGCTCTCTTTCCAGGCATCAAATAATCCACA
CTGGAGAGAAACCTTATGAATGTAATCAGTATGGATAGGCTTTCACATGGAGGGGCAATCTCAGAGCATCCACATTGGAG
AGAAACTTTTATCAATGTAATCAATTTGGATAGGCTTTCACATAAAATTCCACAGTTGCTTCATGTCAGAAAATTCCCAC
TGGAGAGAAACCTCATGAG

Alignment

ORF - retro_mdom_1825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 54.56 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPSQGSITFKDVAVNFTQEEWCLLDHSQKELYREVMLENVQNLLSMELPVHREDFISCFQQKESLWLLEH
          P.S.GSITFK.V.VNF.QEEWCLLDHSQKELYRE.MLENVQNLLSMEL.VHREDFI.CFQQ.ES.WL.EH
Retrocopy PFSTGSITFKEVVVNFPQEEWCLLDHSQKELYREIMLENVQNLLSMELLVHREDFIACFQQRESPWLVEH

Parental  KGPKSSCPEAEANFEVKEMSAKLSLFVEGFGPQRYMNEDPCYFILREMYDSNIKVNKNPKSDCECE-EPA
          KGPK.SCPEAE.NF.VKEMSAKLSLFVE.FGPQR.MN.DPC.FILR.MY.SNIKVNKN.KSDCE.E...A
Retrocopy KGPKNSCPEAEINFKVKEMSAKLSLFVE*FGPQRRMNQDPCDFILRQMYVSNIKVNKNSKSDCEFE<KTA

Parental  EKFSQYSVLNRYIKLNSRNDCWQDSEYSKCFPEEVGFIQSPKK-PEMPTYQGN-PGGMAFGWSLGLIRYP
          EKFSQYSVLN.YIKLNSRNDC.QDSE.SKCFPE.VGFIQSPKK.PEMPTYQ.N.PGGMAFG.SLGLIR.P
Retrocopy EKFSQYSVLNQYIKLNSRNDCCQDSEFSKCFPE*VGFIQSPKKPPEMPTYQDN<PGGMAFG*SLGLIRHP

Parental  KSKCVEVLSVSNKGGKPFSQNSELGSHQIVHTGEKPYECKHCGKAFTVMGSLARHQIIHTGEKPYECKHC
          KSKCVE.LSVSNKGGKPFSQNSELG.HQIVH.GEKPYECKHCGKAFTVMGSL.RHQIIHTGEKPYEC...
Retrocopy KSKCVEMLSVSNKGGKPFSQNSELGLHQIVHNGEKPYECKHCGKAFTVMGSLSRHQIIHTGEKPYECNQY

Parental  GKAFIWRGDLDKHQRIHTGEKPY-ECTQCGKTFTERSNLAKHQRFHTGKKPYE
          G.AF.WRG.L....R..T.E.....C.Q.G..FT..S..A..Q...TG.KP.E
Retrocopy G*AFTWRGNL----RASTLERNFYQCNQFG*AFT*NSTVASCQKIPTGEKPHE

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_1825 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1825 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010049	1 retrocopy	retro_mdom_1825 ,