RetrogeneDB ID: retro_mdom_679

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:79910628..79911876(+)
• Located in intron of: ENSMODG00000007332

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS3
• Ensembl ID: ENSMODG00000004742
• Aliases: None
• Description: COP9 signalosome subunit 3 [Source:HGNC Symbol;Acc:2239]

Sequence

>retro_mdom_679
ATGACGTCTGCCCTGGAGCAATTCGTGAACAGCTCAATGACTCAACTTTGTGAATTGATAAACAAAAGTGGAGAACTTGC
TAGCAAAAAAAACTGATCCCACCTTGATACAGTGCTTGGTGCTTTGGATGCACCAGAGCCTTCCTTGGGGGTCCTTGCAG
TTCTGTTTGTGAAGTTTTCTATGCCCCGTGTGCCTGACTTCGAAACATTATTCTCACAGGTTCAGCTTTTTATCAGCACT
TGTAATGGGGAGCATATTAGATACTCAACAGACACTTTTGCTGGTCTTTGCCACCAGTTAACAAATACTCTCGTGGAAAG
AAAACAGCCCCTGCGAGGAATTGGTACCCTCAGACGAGCCATAGACAAGATGCAGAGGAATACAAACCAACTGACCTCAG
TCCATGCAGACCTCTGCCAGCTTTGTTTATTGGCAAAGTGCTTTAAGCCTGCCCTCCTCTATCTGGATGTGGATATGACG
GACATGTGTAAGGAGAATGGGGCTTCTGATGCAAAGCACTTCTTATGTTACTACTACTATGGTGGGATGATCTACACGGG
GCTAAAGAACTTTGAGAGAGCTCTCTACTTTTATGAGCAAGCCCTGACTACTCCTGCCATGGCACTCAGTCACATTATGC
TGGAATCCTATAAGAAGTATATTCTAGTTTCTTTGATATTACTGGGCAGAGTTCAGCAGCTGCCAAAACACACTTCTCAG
ATTGTTGGTCAATTCATTAAGCCCCTTAGCAATGCTTACCATGAACTAGCACAAGTTTATTCAACCAATAATCCATCAGA
ACTCCGAACTCTGGTAAACAAGCATAGCAAAACTTTCACTAGAGATAACAATATGGGGCTGGTTAAGCAGTGTTTTTCCT
CTATTTATAAGAAGAACATTCAGAGGCTAACAAAGACATGTTTAACGTTGTCATTACAAGACTTGGCAAGTCGTGTACAG
TTGTTAGGACCACAGGAGGCTGAAAAATATGTCCTTCACATGATAGAAGATGGTGAAATTTTTGCAAGTATTAATCAAAA
GGATGGTGTGGTCCGTTTCCATGATAATCCTGAAAAATATAACAATCCAGCTATGCTTCATAACATTGATCAGGAGGTGC
AGAAATGTATAGAGCTTGATGAGCGGCTCAAAGCCATGGATCAAGAAATCACAATGAATCCTCAGTTTGTGCAAAAGAGT
ATAGGCTCCCAAGAAGATGATTCAGAAAGCGAGCCATCCAGTTATTCT

Alignment

ORF - retro_mdom_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.74 %
• Parental protein coverage: 97.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNSVRQLSAQGQMTQLCELINKSGELLAKNL-SHLDTVLGALDVQEHSLGVLAVLFVKFSMPSVPDFETL
          ..S.........MTQLCELINKSGEL......SHLDTVLGALD..E.SLGVLAVLFVKFSMP.VPDFETL
Retrocopy MTSALEQFVNSSMTQLCELINKSGELASXXX*SHLDTVLGALDAPEPSLGVLAVLFVKFSMPRVPDFETL

Parental  FSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRGIGILRQAIDKMQMNTNQLTSIHADLCQ
          FSQVQLFISTCNGEHIRY.TDTFAGLCHQLTN.LVERKQPLRGIG.LR.AIDKMQ.NTNQLTS.HADLCQ
Retrocopy FSQVQLFISTCNGEHIRYSTDTFAGLCHQLTNTLVERKQPLRGIGTLRRAIDKMQRNTNQLTSVHADLCQ

Parental  LCLLAKCFKPALPYLDVDMMDICKENGAYDAKHFLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVS
          LCLLAKCFKPAL.YLDVDM.D.CKENGA.DAKHFLCYYYYGGMIYTGLKNFERALYFYEQA.TTPAMA.S
Retrocopy LCLLAKCFKPALLYLDVDMTDMCKENGASDAKHFLCYYYYGGMIYTGLKNFERALYFYEQALTTPAMALS

Parental  HIMLESYKKYILVSLILLGKVQQLPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFT
          HIMLESYKKYILVSLILLG.VQQLPK.TSQIVG.FIKPLSNAYHELAQVYSTNNPSELR.LVNKHS.TFT
Retrocopy HIMLESYKKYILVSLILLGRVQQLPKHTSQIVGQFIKPLSNAYHELAQVYSTNNPSELRTLVNKHSKTFT

Parental  RDNNMGLVKQCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGM
          RDNNMGLVKQC.SS.YKKNIQRLTKT.LTLSLQD.ASRVQL.GPQEAEKYVLHMIEDGEIFASINQKDG.
Retrocopy RDNNMGLVKQCFSSIYKKNIQRLTKTCLTLSLQDLASRVQLLGPQEAEKYVLHMIEDGEIFASINQKDGV

Parental  VSFHDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGSKPSSYS
          V.FHDNPEKYNNPAMLHNIDQE..KCIELDERLKAMDQEIT.NPQFVQKS.GSQEDDS.S.PSSYS
Retrocopy VRFHDNPEKYNNPAMLHNIDQEVQKCIELDERLKAMDQEITMNPQFVQKSIGSQEDDSESEPSSYS

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_679 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_679 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000004742	1 retrocopy	retro_mdom_679 ,
Nomascus leucogenys	ENSNLEG00000013466	1 retrocopy	retro_nleu_2394,