RetrogeneDB ID: retro_mdom_1995

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:32928846..32929471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSMODG00000017183
• Aliases: None
• Description: nuclear receptor binding factor 2 [Source:HGNC Symbol;Acc:19692]

Sequence

>retro_mdom_1995
CAGCCTGGCTCATCAACAGAACAGCTATTAGCAGCAGGCTATGAAGAGGCTATTTCCTAGCACAAAAGGGCAGCTACCTA
TGTTTTTGAGGCCAGGAAGCTGATACAAATTGAGTAAGCTCAATAATCACTGGAATTACAAAAGCATGGCCACGTGAAGC
AGCTGTAACTTACCTAGGAGAGTCGGAAAAGGGCAACATAGGAAGAAAGGTGGAAAGGCCAAACTAATCCTCCTCACCTG
ACGACACTGTGCAAACCATCTTTCAAAGGTAGGTCTGATGGCCCAGGTAGGCCTGTGTCTCAGAAGTTTGATTCTGCTCC
CAAGAAACGCGTGCCAGAAAAGCCAGGATTCTTTGACAAGGGCTCAAGCACTCTCCTTTTCCTCATTTCAGAAGGGGAAA
GAGCCAACAGAACCACATACCGGTAGCAAAGCTCCCAAAGACAACAAAACAATAATAGGAACCTAAGCAGACAAGATTAC
TGATATGCAGCAACATGCAGTTTCTTGTGGCTAACACTGAAAGACTGCAGGGAGAAAACTGAAGCAAGTCAAAGCTGGAA
AGACCAAACTCCAAAAAGCACCACTAGAAAAGCAATTTGCTGTAGACCTTGACTTTCCAGAAAAA

Alignment

ORF - retro_mdom_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.11 %
• Parental protein coverage: 73.87 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQSRKADRSLAAGKYEEAISCHQKAAAYLSEAMKLTQSEQAQLSLELQRDSHMKQLLLIQERWKRAKREE
          Q........LAAG.YEEAIS.H..AA.Y..EA.KL.Q.E.AQ.SLELQ...H.KQL.L..E..KRA..EE
Retrocopy QPGSSTEQLLAAG-YEEAIS*HKRAATYVFEARKLIQIE*AQ*SLELQKHGHVKQL*LT*ESRKRAT*EE

Parental  RWKAQQTPDGTPHLLTSCKPSAEDGSEGPSGPRPQLLSPAPERLSPAVPGVFDRDPDTLLFLL-QKRKDP
          RWK.Q..P...PHL.T.CKPS....S.GP..P..Q....AP....P..PG.FD....TLLFL..QK.K.P
Retrocopy RWKGQTNP---PHLTTLCKPSFKGRSDGPGRPVSQKFDSAPKKRVPEKPGFFDKGSSTLLFLI>QKGKEP

Parental  TEPCTVSKAPKDDKTIIEEQATKIADLKRHVEFLVADNERLRRENKQLRAEKARLQKAPLEKELDVDADF
          TEP.T.SKAPKD.KTII...A.KI.D...H............R..KQ..A.K..LQKAPLEK...VD.DF
Retrocopy TEPHTGSKAPKDNKTIIGT*ADKITDMQQHAVSCG*H*KTAGRKLKQVKAGKTKLQKAPLEKQFAVDLDF

Parental  VEK
          .EK
Retrocopy PEK

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	136.96 RPM
SRP007412_cerebellum	0.00 RPM	134.83 RPM
SRP007412_heart	0.00 RPM	157.69 RPM
SRP007412_kidney	0.00 RPM	142.22 RPM
SRP007412_liver	0.00 RPM	454.15 RPM
SRP007412_testis	0.00 RPM	310.37 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1995 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1995 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995 ,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,