RetrogeneDB ID: retro_mdom_1344

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:88294321..88295047(-)
• Located in intron of: ENSMODG00000018331

Retrocopy information

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

Parental gene information

• Parental gene symbol: KAT8
• Ensembl ID: ENSMODG00000001856
• Aliases: None
• Description: K(lysine) acetyltransferase 8 [Source:HGNC Symbol;Acc:17933]

Sequence

>retro_mdom_1344
ACCTACCTCAGTCTACATCCTAGTATTTGGCATTCAGCAGAAGTGATTCAGCCCAGGGTGAAGACCAGGAAGGAAGAGAG
GAATTCTACATACATTATATGGGCTTTAACCATGGGCTGGATGAAGGGGTGGTCAAGAGTTGGCTGGCCTTGACCAAGAC
AGTGAAGGAAGCTGTTGAGAGGAACTCTGAGAAGTACCTTAGTGAATTAGCTGAGCAGTCTGAAGGCAAGATCACCTGCA
ACCAGAAACACAAGCATGATAAGATCTTCCATGTGCAGAAGACCTACTTGGAGATGAATCCCATAACAGCAGCACTAGAG
AAGGAACATGAGGCAATTACCAAGGTGAAGTATGTGAGTAAGATTCATATTGGAAATTATGAGATTGATGCCTGGTACTT
CTCCCCATTTCCAGAAGATTATAGGAAACAGCCCAACTTTGGCTCAGTGAATACTACCTCAAATACATGAAGTTTAAGAG
CCACCATTTTTATTTGGGGCAGTGCCAGTGGAGATGGCCACCTAGCAAGGAAATCTACCAAAAGAACAATATCTCGGTGT
ATGAAGTAGATGGCAAGGGCCATAAGATTTATCGCCAGACCTGTGACTGTTGGCCAAGCTATTCCTGGATCACAAGACTC
TTTACTTTGATGTGGAACCATTAGTCTTCTACATCTTGACAGAGGTAGACAGAGAGGGGGCCCACATTGTGGGATACTTC
TCTAAG

Alignment

ORF - retro_mdom_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 59.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TYLCRRPDSTWHSAEVIQSRVN-DQEGREEFYVHYVGFNRRLDEWVDKNRLALTKTVKEAVQKNSEKYLS
          TYL...P.S.WHSAEVIQ.RV..DQEGREEFY.HY.GFN..LDE.V.K..LALTKTVKEAV..NSEKYLS
Retrocopy TYLSLHP-SIWHSAEVIQPRVK<DQEGREEFYIHYMGFNHGLDEGVVKSWLALTKTVKEAVERNSEKYLS

Parental  ELAEQPERKITRNQKRKHDEINHVQKTYAEMDPTTAALEKEHEAITKVKYVDKIHIGNYEIDAWYFSPFP
          ELAEQ.E.KIT.NQK.KHD.I.HVQKTY.EM.P.TAALEKEHEAITKVKYV.KIHIGNYEIDAWYFSPFP
Retrocopy ELAEQSEGKITCNQKHKHDKIFHVQKTYLEMNPITAALEKEHEAITKVKYVSKIHIGNYEIDAWYFSPFP

Parental  EDYGKQP-KLWLCEYCLKYMKFEKSYRFHLGQCQWRQPPGKEIYRKNNISVYEVDGKDHKIYCQ-NLCLL
          EDY.KQP..LWL.EY.LKYMKF.KS..F.LGQCQWR.PP.KEIY.KNNISVYEVDGK.HKIY.Q..L.LL
Retrocopy EDYRKQP<QLWLSEYYLKYMKF-KSHHFYLGQCQWRWPPSKEIYQKNNISVYEVDGKGHKIYRQ<DL*LL

Parental  AKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSK
          AKLFLDHKTLYFDVEP.VFYILTEVDR.GAHIVGYFSK
Retrocopy AKLFLDHKTLYFDVEPLVFYILTEVDREGAHIVGYFSK

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_1344 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1344 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001625	1 retrocopy	retro_mmur_462,
Myotis lucifugus	ENSMLUG00000004779	1 retrocopy	retro_mluc_1916,
Monodelphis domestica	ENSMODG00000001856	1 retrocopy	retro_mdom_1344 ,
Rattus norvegicus	ENSRNOG00000019585	1 retrocopy	retro_rnor_1626,
Sarcophilus harrisii	ENSSHAG00000011739	1 retrocopy	retro_shar_568,