RetrogeneDB ID: retro_mdom_1837

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:53809707..53810001(+)
• Located in intron of: ENSMODG00000020487

Retrocopy information

• Ensembl ID: ENSMODG00000020488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSMODG00000012563
• Aliases: None
• Description: family with sequence similarity 206, member A [Source:HGNC Symbol;Acc:1364]

Sequence

>retro_mdom_1837
GTGGAGGAGGCCGAGCTCACCATGGCGGCTGATGCTGGAGGCGTTTCTCCGGCAGTCCCATCACTGGCGGATCGCTACTT
CACCCGCTGGTACAAGGCTGATGCTAAGGGAAGGTCGTGTGAGCATCACTGTATTTTGCAGCACTCTAACAGAATCTGTG
TAATCACATTGGCAGAATCTCATCCACTTCTTCAAAATGGAAAAACAATTAAGAGTATTAATTACCAAATTAGTGCCAAC
TGTAGCCGACTTCAGAACAAAGTTTCTGGGAAGTTTAAGCGGGATATCCTGTTC

Alignment

ORF - retro_mdom_1837 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEAELTMAADAGGVSPAVPSLVDRYFTRWYKADVKGKPGEDHCILQHSNRQIGICVITLAESHPLLQNG
          .EEAELTMAADAGGVSPAVPSL.DRYFTRWYKAD.KG...E.HCILQHSNR...ICVITLAESHPLLQNG
Retrocopy VEEAELTMAADAGGVSPAVPSLADRYFTRWYKADAKGRSCEHHCILQHSNR---ICVITLAESHPLLQNG

Parental  KTIKSINYQISANCSRLQNKVSGKFKRGAQF
          KTIKSINYQISANCSRLQNKVSGKFKR...F
Retrocopy KTIKSINYQISANCSRLQNKVSGKFKRDILF

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_1837 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1837 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837 ,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,
Tupaia belangeri	ENSTBEG00000004984	2 retrocopies	retro_tbel_2689, retro_tbel_385,