RetrogeneDB ID: retro_mdom_1513

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:86927018..86927828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012675
• Aliases: None
• Description: None

Sequence

>retro_mdom_1513
TCTTCCATGCAGCTGCTCAGCTCAAAGCATGTGTCCAGACTCTGAGAAGAGCAGGAAAAGATAGTCACTGACTGCCAAGA
AAAGATCCAGCATTGAATGAAGGTAGAACATGATTATGAGGCTTTTTAAGAAAGACTCATCACATTGCCTGATAAAGTCT
CTTATGACATTATGGTATCTTTTGGTCCTCTTGCCTTCATGCCCAGACAACTTGTTAGTACCAATAAAGTCATGATTTTA
CTTCGGAACAACTGGTTTTGCAAGTGCTCAGCAAAGCAGGCCATAGGTTTAATAGAACACAGGAAAAATGTTTGAAAAAC
ACTGTATAATTTAAAGAAAGTGATGAAGAACTTTGAATCCAGAGTTGAATTCACAGAGGACTTAAAAAGAATGAGTCATG
TAGCAGGTGATATTATTGATATAAGAAAAGACATTAAAACTGACATTGAAGTTAAAGGAAAGCACAGAACTGTTCATAAG
ACCTCATTCAAAACCAAAAACTTTAGTTGTATTTGAAGCAGATTTTTTAGATGACTCAAAATCCAAAGACAACCTCCTCA
GGAGAAGGAACTATGGGCTTGACTTGAGGAGCTAGAAAGACAAGAAGATCTTTTGGGTGAACTCAATAGAAAAACTGATA
CTTTGTTTGCAAATGGAGAAGATATGACTTCTTCTGAAGAGGAGAAGGAAGATCAAAAGACAGATTTCATGAAACACAGA
ATAACAGATTCTCTTACTCAGGGCAGTTTTCAAAAGGACATTCCAAATTCCAAATTACTCAATGGTCAAGTAAATGGTTC
AAGTTCTTAT

Alignment

ORF - retro_mdom_1513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 53.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSTQPLRSEHVARLREEQEKVVTGCQEKIQHWRKVEHDYEALQERLSTLPDKLSYDIMVPFGPLAFMPGQ
          SS.Q.L.S.HV.RL.EEQEK.VT.CQEKIQH..KVEHDYEA..ERL.TLPDK.SYDIMV.FGPLAFMP.Q
Retrocopy SSMQLLSSKHVSRL*EEQEKIVTDCQEKIQH*MKVEHDYEAF*ERLITLPDKVSYDIMVSFGPLAFMPRQ

Parental  LVSTNEVTVLLGDNWFCKCSAKQAVGLVEHRKKHVRKALDDLKKVMKNFESRVEFTEDLKRMSDAAGDIV
          LVSTN.V..LL..NWFCKCSAKQA.GL.EHRK..V.K.L..LKKVMKNFESRVEFTEDLKRMS..AGDI.
Retrocopy LVSTNKVMILLRNNWFCKCSAKQAIGLIEHRK-NV*KTLYNLKKVMKNFESRVEFTEDLKRMSHVAGDII

Parental  DIREDIKNDIEVKGKHRTAHK-PHSKPKTLDVFEADFVDDSKSKDNFL-SEKELWARLDELERQEDLLGE
          DIR.DIK.DIEVKGKHRT.HK.PHSKPKTL.VFEADF.DDSKSKDN.L..EKELWA.L.ELERQEDLLGE
Retrocopy DIRKDIKTDIEVKGKHRTVHK>PHSKPKTLVVFEADFLDDSKSKDNLL<QEKELWA*LEELERQEDLLGE

Parental  LSRKSDTLFANGEDMTSSEEEKEDQKTDVMKHRITDSFTQGSFQKDITNSKLLNGQVNGSSSY
          L.RK.DTLFANGEDMTSSEEEKEDQKTD.MKHRITDS.TQGSFQKDI.NSKLLNGQVNGSSSY
Retrocopy LNRKTDTLFANGEDMTSSEEEKEDQKTDFMKHRITDSLTQGSFQKDIPNSKLLNGQVNGSSSY

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	76.05 RPM
SRP007412_cerebellum	0.00 RPM	79.98 RPM
SRP007412_heart	0.00 RPM	65.99 RPM
SRP007412_kidney	0.00 RPM	79.01 RPM
SRP007412_liver	0.00 RPM	88.61 RPM
SRP007412_testis	0.00 RPM	123.95 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1513 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1513 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001823	1 retrocopy	retro_cjac_2693,
Monodelphis domestica	ENSMODG00000012675	1 retrocopy	retro_mdom_1513 ,
Pongo abelii	ENSPPYG00000009810	1 retrocopy	retro_pabe_547,
Pan troglodytes	ENSPTRG00000010784	1 retrocopy	retro_ptro_3086,