RetrogeneDB ID: retro_mdom_1392

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:268966410..268966817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSMODG00000015478
• Aliases: None
• Description: family with sequence similarity 3, member C [Source:HGNC Symbol;Acc:18664]

Sequence

>retro_mdom_1392
GCTGTAAAGTTGGTGGTTGCTGTAGCAGTATTTCTACTGACATTTTATGTTATATCTCAAGTATTTGAAATAAAGCTAGA
TTCAAACTTAGGATATTTATTTGCAAGGTCAGCATTGCAGAGAGCTTATACAAAACCTCCCAGGTATAAATGTGGGATTT
CAAAAGCTTGTCCAGAAAAATATTTTGCCTTCAAAATGGCAAGTGGAATGTTTTTGGCCCCAAAATTTGTGTGGAAAACA
ATATTTTAATGAGTGGTGTAAAGAATAATGTTGGAAGAGGAATCAATGTTGCCTTGGTAAATGGAAAAACAGGAGAAGCA
TTAAGCACTGAATACTTTGATATGTGGGGAGGAGATGTGGCACCATTTATTGGATTCCTTAAGTCTATTCCAGATGGAAC
CATAGTT

Alignment

ORF - retro_mdom_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVKLVVAVAVFLLTFYVISQVFEIKLDSNLGNLFARSALQIAYTKPPRYKCGISKACPEKHFAFKMASGA
          AVKLVVAVAVFLLTFYVISQVFEIKLDSNLG.LFARSALQ.AYTKPPRYKCGISKACPEK.FAFKMASG.
Retrocopy AVKLVVAVAVFLLTFYVISQVFEIKLDSNLGYLFARSALQRAYTKPPRYKCGISKACPEKYFAFKMASGM

Parental  ANVVGPK-ICVEDNILMSGVKNNVGRGINVALVNGKTGEALRTEYFDMWGGDVAPFIEFLKSIPDGTIV
          .....PK.ICVE.NILMSGVKNNVGRGINVALVNGKTGEAL.TEYFDMWGGDVAPFI.FLKSIPDGTIV
Retrocopy --FLAPK<ICVENNILMSGVKNNVGRGINVALVNGKTGEALSTEYFDMWGGDVAPFIGFLKSIPDGTIV

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_1392 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1392 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000009016	1 retrocopy	retro_mdom_1371,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392 ,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,