RetrogeneDB ID: retro_mdom_1623

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:217857524..217857944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KXD1
• Ensembl ID: ENSMODG00000003489
• Aliases: None
• Description: KxDL motif containing 1 [Source:HGNC Symbol;Acc:28420]

Sequence

>retro_mdom_1623
GACCAGTTTGAGAAAACCAATGAAATGGTCTTGAACTTTAACAAACTGTCCAACATCTACATGCAGCACATGAGTGAGCA
TTTCACACACCAGTCCAAGACAATGATGGAGATGAGGAAGGACCTGGACAGTATCTACTTCAGGCTCCAGACTCTGAAAA
TCAAGCTGTCAAAGGAGTACCAAAATGCTTTTAATCATATCCATGAGTCTCCCATCCCAGAGGAGGAGGAAGATGATGAC
GTGTACCTCACCCCGGCCAGCCCGGCTACCACCATTGCTACCTCAGAGCAGAGTAAGAGGTCCTGTGACCCAAGCCCAGA
TATCACCTCTCCAGTTCTGAGCCCATTCTCTGAAGATTTATCCCAAGAGAACCTGGACTCTCCAGATGTGAATAAGGAGA
GCCTGACAGGTGCTGAGGAT

Alignment

ORF - retro_mdom_1623 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.86 %
• Parental protein coverage: 73.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRFEKTNEMLLNFNNLSNVRMQQMSERFTHHTRTLMEMKKDLDSIFRRLRTLKAKLSKQYPDAFSYIHES
          D.FEKTNEM.LNFN.LSN..MQ.MSE.FTH...T.MEM.KDLDSI..RL.TLK.KLSK.Y..AF..IHES
Retrocopy DQFEKTNEMVLNFNKLSNIYMQHMSEHFTHQSKTMMEMRKDLDSIYFRLQTLKIKLSKEYQNAFNHIHES

Parental  PI-LEEEDDDVDPVPASSATTIATSEQSTGSCDTSPDIISPVLSPDFEDLSQGRLDSPAVNGESLTGDED
          PI..EEEDDDV...PAS.ATTIATSEQS..SCD.SPDI.SPVLSP..EDLSQ..LDSP.VN.ESLTG.ED
Retrocopy PIPEEEEDDDVYLTPASPATTIATSEQSKRSCDPSPDITSPVLSPFSEDLSQENLDSPDVNKESLTGAED

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_1623 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1623 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623 ,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117, retro_mmus_3557, retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808, retro_rnor_812,