RetrogeneDB ID: retro_mdom_1385

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:222827449..222828233(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C21orf33
• Ensembl ID: ENSMODG00000021082
• Aliases: None
• Description: chromosome 21 open reading frame 33 [Source:HGNC Symbol;Acc:1273]

Sequence

>retro_mdom_1385
ATGTTTGCTGTGAGGTTTGTGGCGGCCTCCAGGCCTGTTTTGCCAGTCTGTCTGCCCTGGCTGAGGTCCAGAGGTCGGCA
TCTTATTCCCGTTGCTGGCTTTCATGGCTCTGCGCTGCATCCTGGGGCTAAAGTAGCTGTTATTTTTTTCTGGATGTGGT
GTCTATGATGGCACAGAAATTCATGAGGCCTCAGTGATATTGGTTCACTTGAGTCATGAAGGTGCTGAAGTTAAGATGTA
TGCACCTAATGTTCCTCAGATGCATGCCATCAATCATACCAAAGGACAACCAACAGAGAGTGAAAAATGAAATGCATTGG
TAGACTCAGCAAGGATTGCCCGAGGCAAGATTGCTGAATTGTCAGAACTTAAGTCAAAGGATTTTGATGCTGTTATCTTT
CCTGGGGGATTTGGAGCTGCCAAAAAACTGTGTACATTTGCAGTCGATGGAAAAGATTGTAAAGTCAACAAAGATGTTGA
ATGAATTCTAAATGAGTTCCATAAAGAAGGGAAACCAATTGGCTTGTGCTGCATTTCCCCAGTTCTTGCAGCCGAAGTAC
TTACAGTTACAGAAGAGACAGTAGGACATGAGCAGGCAGAAGGTGGGAAATGGCTTTATTGTGAAACTGCAGAAGCCATT
AAAGACTTGGGAGCAAAGCACTGTGTGAAAGAAGTAACTGAAGCTCACGTAGACTCTAAGAACAAAGTGGTCACGACTCC
AGCTTTTATGTGTGAAACAGGATTGCACCATATTTTTGATGGAATTGAGATAATGTGTTGAAAC

Alignment

ORF - retro_mdom_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.84 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFAVRFAAASRPVLPVCLPWLRSGGRHHTPVAGFHGSALRPGAKVAVIF-SGCGVYDGTEIHEASAILVH
          MFAVRF.AASRPVLPVCLPWLRS.GRH..PVAGFHGSAL.PGAKVAVIF.SGCGVYDGTEIHEAS.ILVH
Retrocopy MFAVRFVAASRPVLPVCLPWLRSRGRHLIPVAGFHGSALHPGAKVAVIF>SGCGVYDGTEIHEASVILVH

Parental  LSREGAEVKMYAPNVPQMHVIDHTKGQPTESEKRNALVESARIARGKIAELSELKSKDFDAVIFPGGFGA
          LS.EGAEVKMYAPNVPQMH.I.HTKGQPTESEK.NALV.SARIARGKIAELSELKSKDFDAVIFPGGFGA
Retrocopy LSHEGAEVKMYAPNVPQMHAINHTKGQPTESEK*NALVDSARIARGKIAELSELKSKDFDAVIFPGGFGA

Parental  AKNLCTFAVDGKDCKVDKDVERILNEFHKEGKPIGLCCISPVLAAKVLKGTEVTVGHEQAEGGKWPYCET
          AK.LCTFAVDGKDCKV.KDVE.ILNEFHKEGKPIGLCCISPVLAA.VL..TE.TVGHEQAEGGKW.YCET
Retrocopy AKKLCTFAVDGKDCKVNKDVE*ILNEFHKEGKPIGLCCISPVLAAEVLTVTEETVGHEQAEGGKWLYCET

Parental  AEAIKALGAKHCVKEVTEAHVDSKNKVVTTPAFMCETGLHHIFDGIGIMVHN
          AEAIK.LGAKHCVKEVTEAHVDSKNKVVTTPAFMCETGLHHIFDGI.IM..N
Retrocopy AEAIKDLGAKHCVKEVTEAHVDSKNKVVTTPAFMCETGLHHIFDGIEIMC*N

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_1385 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1385 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001007	1 retrocopy	retro_mmur_1540,
Monodelphis domestica	ENSMODG00000021082	1 retrocopy	retro_mdom_1385 ,