RetrogeneDB ID: retro_mdom_2016

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:36942655..36943000(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDCD2
• Ensembl ID: ENSMODG00000007641
• Aliases: None
• Description: NudC domain containing 2 [Source:HGNC Symbol;Acc:30535]

Sequence

>retro_mdom_2016
GGTACTCTCCAAGAGCAGCTGGGAGCAGAGGGAAGCATGTCTGCACCATTTGTGGAGCAAAACAGGATGGTGCCTTGCGG
GATACCCTGGGGCCAGTGGTGCCAGTCCCTGGAGGAGGTGTTCATCGAAGTCTGGGTGCCACCGGGCACTCGCGTGCAGG
AGATCCAGTGTGGCCTGCAGAGTCGGCATGTGGAGCTCGCTGTGTGGGGCCAGGAGATCCTCAAGGGCAAACTCTTTGAT
TCTACAGTAGCTGATGAGGGAACGTGGACATTAGAGGACAGAAAAATGGTTCCTGTAGTTCTTACCAAGACAAAGAGATA
TGTAGCAAATTGTTGGGCCTCTCTT

Alignment

ORF - retro_mdom_2016 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 60.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTLRGQLGAEGSMSAPFEERSGVVPCGTPWGQWYQTLEEVFIEVQVPPGTRAQEIQCGLQSRHVELAVRG
          GTL..QLGAEGSMSAPF.E....VPCG.PWGQW.Q.LEEVFIEV.VPPGTR.QEIQCGLQSRHVELAV.G
Retrocopy GTLQEQLGAEGSMSAPFVEQNRMVPCGIPWGQWCQSLEEVFIEVWVPPGTRVQEIQCGLQSRHVELAVWG

Parental  QEILKGKLFDSTIADEGTWTLEDRKMVRIVLTKTKRDAANCWTSL
          QEILKGKLFDST.ADEGTWTLEDRKMV..VLTKTKR..ANCW.SL
Retrocopy QEILKGKLFDSTVADEGTWTLEDRKMVPVVLTKTKRYVANCWASL

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	26.46 RPM
SRP007412_cerebellum	0.00 RPM	18.61 RPM
SRP007412_heart	0.00 RPM	20.93 RPM
SRP007412_kidney	0.00 RPM	19.75 RPM
SRP007412_liver	0.00 RPM	30.71 RPM
SRP007412_testis	0.00 RPM	25.14 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2016 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2016 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005270	1 retrocopy	retro_amel_535,
Bos taurus	ENSBTAG00000014772	1 retrocopy	retro_btau_1735,
Callithrix jacchus	ENSCJAG00000015367	1 retrocopy	retro_cjac_2093,
Cavia porcellus	ENSCPOG00000000877	1 retrocopy	retro_cpor_936,
Dipodomys ordii	ENSDORG00000014291	1 retrocopy	retro_dord_188,
Macropus eugenii	ENSMEUG00000004802	1 retrocopy	retro_meug_1673,
Myotis lucifugus	ENSMLUG00000001670	1 retrocopy	retro_mluc_1154,
Monodelphis domestica	ENSMODG00000007641	2 retrocopies	retro_mdom_1058, retro_mdom_2016 ,
Ornithorhynchus anatinus	ENSOANG00000021414	1 retrocopy	retro_oana_122,
Oryctolagus cuniculus	ENSOCUG00000005783	1 retrocopy	retro_ocun_819,
Otolemur garnettii	ENSOGAG00000024929	3 retrocopies	retro_ogar_1486, retro_ogar_1696, retro_ogar_482,
Sarcophilus harrisii	ENSSHAG00000007551	1 retrocopy	retro_shar_559,
Ictidomys tridecemlineatus	ENSSTOG00000028665	1 retrocopy	retro_itri_1770,
Tupaia belangeri	ENSTBEG00000000307	1 retrocopy	retro_tbel_507,
Tarsius syrichta	ENSTSYG00000008090	1 retrocopy	retro_tsyr_1638,