RetrogeneDB ID: retro_mdom_496

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:58290870..58291465(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC94
• Ensembl ID: ENSMODG00000000841
• Aliases: None
• Description: coiled-coil domain containing 94 [Source:HGNC Symbol;Acc:25518]

Sequence

>retro_mdom_496
GCTCCCTTCAACCTGAAATGTAAGACATGTGGGGAGTATATTTACAAAGGCAAGAAATTTAATGCCTGCAAAGAGACCAT
GCAGAAGGAGCTCTATCTGGGACTCCCAATTTTTTGTTTTTATGTCAGGTGTCCCCGATGTCTAGCTGAAATCACCTAAA
AAACAGACCCTGAGAATACAGATTATGCCATGGATCATGAAGCCACTAAGAACTTCCAGGCTGAGAAACTGCTGGAAGAA
GAGAAAAGAGTCCAAAAGCAAAGAGAAGAGGAAGAAGTCAATAACCCTATGAAGGTGCTGGAGAATCAGACCAAGGACTC
CAAGCTGGAGATGGAGGTCCTGGATAATCTGCAGAAGCTGAAGGAGCTCAACCAGCACCAGGCCAATGTGGACTTTGAAG
CCATGTTGCAGCAGTGCCTGCAGTCTGAGGAATAGAAAAGGCAGAGCCAGCAGGAAGAGGACCAGAAGGAAATGGAAGCC
ATGATGGCCCAAGCCAGGACAAGAAGACCCACTGAAGACTGCCTCCAATGAAGAGCCCACTCTGGCCCCTTGCTGGCTGC
CCATTTGGGCCAAGCCCATAGCCATCTTAGAGGAG

Alignment

ORF - retro_mdom_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.12 %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APFNMRCKTCGEYIYKGKKFNARKETVQNELYLGLPIFRFYIKCTRCLAEITFKTDPENTDYTMEHGATR
          APFN..CKTCGEYIYKGKKFNA.KET.Q.ELYLGLPIF.FY..C.RCLAEIT.KTDPENTDY.M.H.AT.
Retrocopy APFNLKCKTCGEYIYKGKKFNACKETMQKELYLGLPIFCFYVRCPRCLAEIT*KTDPENTDYAMDHEATK

Parental  NFQAEKLLEEEEKRVQKEREDEELNNPMKVLENRTKDSKLEMEVLENLQELKELNQRQANVDFEAMLQQY
          NFQAEKLL.EEEKRVQK.RE.EE.NNPMKVLEN.TKDSKLEMEVL.NLQ.LKELNQ.QANVDFEAMLQQ.
Retrocopy NFQAEKLL-EEEKRVQKQREEEEVNNPMKVLENQTKDSKLEMEVLDNLQKLKELNQHQANVDFEAMLQQC

Parental  RVSEEEKRQREQEEDQREMEAMMEQSRKRRLIED-SDSDEEPIPAPSQLLIRANPTAILEE
          ..SEE.KRQ..QEEDQ.EMEAMM.Q.R.RR..ED.....E.P..AP..L.I.A.P.AILEE
Retrocopy LQSEE*KRQSQQEEDQKEMEAMMAQARTRRPTED>ASNEE-PTLAPCWLPIWAKPIAILEE

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	0.72 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	1.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	2.75 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_496 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_496 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022785	1 retrocopy	retro_ecab_347,
Monodelphis domestica	ENSMODG00000000841	1 retrocopy	retro_mdom_496 ,
Mus musculus	ENSMUSG00000003208	1 retrocopy	retro_mmus_1640,
Otolemur garnettii	ENSOGAG00000001662	1 retrocopy	retro_ogar_168,
Sarcophilus harrisii	ENSSHAG00000010428	1 retrocopy	retro_shar_394,