RetrogeneDB ID: retro_mdom_1269

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:200859535..200860527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006756
• Aliases: None
• Description: None

Sequence

>retro_mdom_1269
AAGATGATTTCCTTTGCGCCTGTCTCAGTGCTGTTGAAGCAGCGGCTATAGACTGTAGCTGTTGTTCAGTGGGTTTTCAG
TTTCCTGACTATGGGCATAGTCTGCACAGTCATCTTCATTGACCTTTTCTTCACCCGCTTTTGGTTCCTCAGAATGCTAT
ATTCAGCCTGGTGGTACCTGGAAAGAAATACCCCAAGAGAAGGTGGGACACAGATCCAGACCATGAAGTGATAGCATGTG
TGGAAGTACCCGGCAGACTACTTTCCTGTCTCACTCATCAAGACAGTGGATTTGGTTCCAACACAGAACTCTATTGCTGA
CGGTGTCCCGGCTACTGGAGCTTTCACCAACTTCTGTACTGAAGGCACCAGTTTTTCTTCTGTATTTCCTGGGATCCATT
CCCACCTGATGATGCTGACTTTGGGGTTCTGAATTCCCATCTTCAGGGATTATATCATTAGTGGAGGTTTAGTCACTTCA
GAGAAGGAGTGTGTCTCATATTTGCTGAGCAAGAAGGGAGGTGGAAACTTGCTGGTGATTATTGTGGGAAGGATCCAGGA
GGCCCTGATGCCTGGCCTGGAAGCTACACATTACTGCTGAGGAACTGGAAAGGATTTATTAAACTTGCCTTGTTTCATGG
GGCATCTCTGCTGCCTGTATTCTCCTTTGGGGAGAATGAACTCTTTGACCAAATGGACAATCCTTCAGGATCATGGCTTT
GATGGATCTAGGAAAAACTGCAGAAGGTCATGGGCATCTCCCTCCTAGTCTTCCATGGCCGGGGGATCTTCCAATACAGT
TTTGGCCTGCTCCCTTTCCAGCGGTAAATCTCTACTGTAGTGGGGAAGCCCATCAAGGTGAAGCAAAATATTAACCCAAT
GTCAGATGAAGTGGACCATCTGCATCAGCAGCACATGACAGAATTGTGCAACCTCTGTGAAGCCCTCAAGATTAAATACA
ATGTCCCCCCAGAGCAGCACCTGGAATTCAGA

Alignment

ORF - retro_mdom_1269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMISFAPLSVPLKRRLQTLAALQWVFSFLGLGIVCVVIFIGLFFTRFWFLSMLYSAWWYLDRDTPRKGGR
          KMISFAP.SV.LK.RL.T.A..QWVFSFL..GIVC.VIFI.LFFTRFWFL.MLYSAWWYL.R.TPR.GG.
Retrocopy KMISFAPVSVLLKQRL*TVAVVQWVFSFLTMGIVCTVIFIDLFFTRFWFLRMLYSAWWYLERNTPREGGT

Parental  QIQTIKRWCVWKYLADYFPVSLIKTVDLDPTQNYIAGFHPHGVLATGAFTNFCTEATGFSSVFPGIRPHL
          QIQT.K...VWKY.ADYFPVSLIKTVDL.PTQN.IA.....GV.ATGAFTNFCTE.T.FSSVFPGI..HL
Retrocopy QIQTMK**HVWKYPADYFPVSLIKTVDLVPTQNSIAD----GVPATGAFTNFCTEGTSFSSVFPGIHSHL

Parental  MMLTLWFRIPFFRDYIMSGGMFTSEKECVSYLLSKKGGGNLMVIIVGGAQEAL-DARPGSYTLLLRNRKG
          MMLTL.F.IP.FRDYI.SGG..TSEKECVSYLLSKKGGGNL.VIIVG..QEAL.DA.PGSYTLLLRN.KG
Retrocopy MMLTLGF*IPIFRDYIISGGLVTSEKECVSYLLSKKGGGNLLVIIVGRIQEAL<DAWPGSYTLLLRNWKG

Parental  FVKLALLHGASLLPIFSFGENELFDQMDNPSGSWLRWIQEKLQKVMGISLPVFHGRGIFQYSFGLLPYRR
          F.KLAL.HGASLLP.FSFGENELFDQMDNPSGSWL.WI.EKLQKVMGISL.VFHGRGIFQYSFGLLP..R
Retrocopy FIKLALFHGASLLPVFSFGENELFDQMDNPSGSWL*WI*EKLQKVMGISLLVFHGRGIFQYSFGLLPFQR

Parental  QITTVVGKPIKVKQNINPSSDEVDRLHQQYMTELCNLFETHKIKYNVPPEQHLEFR
          .I.TVVGKPIKVKQNINP.SDEVD.LHQQ.MTELCNL.E..KIKYNVPPEQHLEFR
Retrocopy *ISTVVGKPIKVKQNINPMSDEVDHLHQQHMTELCNLCEALKIKYNVPPEQHLEFR

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_1269 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1269 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001166	1 retrocopy	retro_meug_442,
Monodelphis domestica	ENSMODG00000006756	3 retrocopies	retro_mdom_126, retro_mdom_1269 , retro_mdom_712,
Sarcophilus harrisii	ENSSHAG00000001147	1 retrocopy	retro_shar_583,