RetrogeneDB ID: retro_mdom_1405

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:319508705..319509233(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC10
• Ensembl ID: ENSMODG00000013827
• Aliases: None
• Description: zinc finger, CCHC domain containing 10 [Source:HGNC Symbol;Acc:25954]

Sequence

>retro_mdom_1405
ATTAGAGTGGTCCTGGTTCTCACTAAGATGGCGACTCCCATGCACCGACTTATCACCTGGAGGCAGGCAGAAGCAAATAA
GCAACATGTGAGATGTCAGAAATGTTTATAATTTGGACATTGGACATATGAATGCACAGGAAAAAGAAAATACTTGCATA
GACCTTCAAGAACAGCAGAACTTAAGAAAGCTTTAAAAGAAAAAGAAAACATTATTATTACAACAAAGCATTGGAGAAAC
TAATATAGAAAAAAAGGCCAAGAAAAAAAGATCTAAGAGTGTTACCAGTTCCAGCAGCAGTACCAGTGGAAATTGTCAGT
GACTTCATCAGAGAGTGAAGACTCCTCTACCTCTTCTTCCTCTGAGAGTGATACTGAGGAAACCTCTTCTACTTCATCCT
CATCAACCTCCTCAACTAGTTCTTCCTCTTCGTCTGATTCTGAGTCAGATTTCAGCTCTTCCTCCAGCACCAACTCTACC
ACAGATAGCAGCTCTGATGATGAGCCACCAAAGAAGAAGAAAAAGAAA

Alignment

ORF - retro_mdom_1405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.45 %
• Parental protein coverage: 82.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IAVVPVLAKMATPMHRLIARRQAEANKQHVRCQKCLEFGHWTYECTGKRKYLHRPSRTAELKKALKEKEN
          I.VV.VL.KMATPMHRLI..RQAEANKQHVRCQKCL.FGHWTYECTGKRKYLHRPSRTAELKKALKEKEN
Retrocopy IRVVLVLTKMATPMHRLITWRQAEANKQHVRCQKCL*FGHWTYECTGKRKYLHRPSRTAELKKALKEKEN

Parental  -RLLLQQSIGETNIEKKSKKKRSKSVTSSSSSSSGSS-ASDSSSESEDSSTSSSSDDSDTEETSSTSSSS
          ..LL.Q.SIGETNI........SKSVTSSSSS.SG......SS.....S..SSS...SDTEETSSTSSSS
Retrocopy >LLLQQ-SIGETNIXXXXXXXXSKSVTSSSSSTSGNC<SVTSSESEDSSTSSSS--ESDTEETSSTSSSS

Parental  PSSTSSSSSSDSESDSSSSSSTSSSTDSSSDDEPPKKKKKK
          .SSTSSSSSSDSESD.SSSSST.S.TDSSSDDEPPKKKKKK
Retrocopy TSSTSSSSSSDSESDFSSSSSTNSTTDSSSDDEPPKKKKKK

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	88.68 RPM
SRP007412_cerebellum	0.00 RPM	66.27 RPM
SRP007412_heart	0.00 RPM	36.08 RPM
SRP007412_kidney	0.00 RPM	39.50 RPM
SRP007412_liver	0.00 RPM	53.87 RPM
SRP007412_testis	0.00 RPM	76.02 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1405 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1405 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405 ,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,