RetrogeneDB ID: retro_mdom_1643

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:24603890..24604178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCYT1A
• Ensembl ID: ENSMODG00000018432
• Aliases: None
• Description: phosphate cytidylyltransferase 1, choline, alpha [Source:HGNC Symbol;Acc:8754]

Sequence

>retro_mdom_1643
TGCATCCATGCCAGAATTAAGGAAGATTCGGCACCTGCTCAGTACAGAGTCAGATGATATGCCTACATTCACAAATATTT
TGCCAGAGAATATGAAAAATAAACGTAAAGAAATGGGGTTTGATTAATATCAACTGTTATGACAAGTAGTGATTGGAGAA
GAAATAGGTAGAGGAATAAGGATCGCTACTCAGTGTTTCTGGGATAGTGACACAGACAACGGCACTTACGATGTTTTTAA
GAATGACAGTTTGTTCTGTCTTGTAGCTGCCTTGGCTGTTTCTACCAT

Alignment

ORF - retro_mdom_1643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.2 %
• Parental protein coverage: 73.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CIHTILKEELATAQY-EPSEMPALTKYLSESIKNKLKEMGFDRYKMVVQVVIGEQRGEGVNMAARCFWDA
          CIH...KE..A.AQY.E...MP..T..L.E..KNK.KEMGFD.Y....QVVIGE..G.G...A..CFWD.
Retrocopy CIHARIKEDSAPAQY>ESDDMPTFTNILPENMKNKRKEMGFD*YQLL*QVVIGEEIGRGIRIATQCFWDS

Parental  DTDNYTHDVFMNDSLFCVVAA-FGCFYY
          DTDN.T.DVF.NDSLFC.VAA..GCFY.
Retrocopy DTDNGTYDVFKNDSLFCLVAA<LGCFYH

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_1643 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1643 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
Choloepus hoffmanni	ENSCHOG00000010073	1 retrocopy	retro_chof_33,
Monodelphis domestica	ENSMODG00000018432	1 retrocopy	retro_mdom_1643 ,