RetrogeneDB ID: retro_mdom_1799

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:151886251..151886595(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNRD1
• Ensembl ID: ENSMODG00000016023
• Aliases: None
• Description: zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:13182]

Sequence

>retro_mdom_1799
CTCTTTGCCATAGACCCTGCTTCAGTCTCCTCCAGTTTCCATTCCAAGTCAGATTTCTAACCACAAGATGGCTCAAGTTT
TGGCACTCCTGGAACTTTGGGCATAGTTACCTGCTCCAGTTATGCTTTTTCATAGACTTGCAGGAGTTTGAAGGGAAGGT
GCTAGAGACCTCAGTCATGTCCCACAAAATAGCTTTCATTATGTCAGAGGAAGAATAGCCTGAGTTCCAGGGGCCAATGA
TCAAAAAGAGCTGTTCCAGCTATGACCATGAAGGAATGGCATATCACACCTGACAGACACTCTCCGCTGATGAAATACAG
ACTGTCTTACATATCTTCACTAAC

Alignment

ORF - retro_mdom_1799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.18 %
• Parental protein coverage: 98.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFTMDPPPVSSSFHSDSDFCPECGSILPLPGTLDIVTCPRCGFS-IDVREFEGKVVETSVEFHKLGTTAF
          LF..DP..VSSSFHS.SDF.P..GS....PGTL.IVTC....FS.ID..EFEGKV.ETSV..HK....AF
Retrocopy LFAIDPASVSSSFHSKSDF*PQDGSSFGTPGTLGIVTCSSYAFS<IDLQEFEGKVLETSVMSHKI---AF

Parental  LVSEEEGPEFQGPVIDRRCSNCGHEGMAYHTRQMRSADEGQTVFYTCTN
          ..SEEE.PEFQGP.I...CS...HEGMAYHT.Q..SADE.QTV....TN
Retrocopy IMSEEE*PEFQGPMIKKSCSSYDHEGMAYHT*QTLSADEIQTVLHIFTN

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_1799 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1799 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007328	2 retrocopies	retro_chof_1997, retro_chof_2061,
Dasypus novemcinctus	ENSDNOG00000015720	9 retrocopies	retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726, retro_dnov_1798, retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
Myotis lucifugus	ENSMLUG00000007272	1 retrocopy	retro_mluc_126,
Monodelphis domestica	ENSMODG00000016023	1 retrocopy	retro_mdom_1799 ,
Mustela putorius furo	ENSMPUG00000007474	1 retrocopy	retro_mputfur_968,
Rattus norvegicus	ENSRNOG00000000779	1 retrocopy	retro_rnor_978,
Sorex araneus	ENSSARG00000009716	2 retrocopies	retro_sara_431, retro_sara_745,
Sarcophilus harrisii	ENSSHAG00000001554	1 retrocopy	retro_shar_796,