RetrogeneDB ID: retro_mdom_558

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:297794389..297794794(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CPSF4L
• Ensembl ID: ENSMODG00000025672
• Aliases: None
• Description: cleavage and polyadenylation specific factor 4-like [Source:HGNC Symbol;Acc:33632]

Sequence

>retro_mdom_558
CCACTCATGCTTCTGACCCCGGTGGCTGTGTGCACCTTCTTTCTTAAAGGCTTCTGTGAGAAAGGCCAGCTCTGTCCCTT
TCAGCATGATGATGGGGCAAAGACAGTAGTGTGCAAACACTGGCTTCGGGGGCTTTGTAAGAAGAGTGACCATTCCAAAT
TTTTGCACCAATATGACATCACCAAGATGCCTGAGTGCTACTTCTACTCCAAATTTGGAGAATGCAGCAATAAAGAATGC
CTTTTTCTTCATGCTGACCCAGCCTTCAAGATCCGAGACTGTCCCTGGTATGACCAAGGTTTCTGTAAGTATAGTCTTCT
GTGTAAATTCCGCCATAACAGAAGACTGTTGTGTACCAGCTACTTAGTTGGCTTCTGTCCAGAAGGACATGATTACAAAT
TCACA

Alignment

ORF - retro_mdom_558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGMDKSGVAVCTFFLKGFCEKGQLCPFRHDDGEKTVVCKHWLRGLCKKSDHCKFLHQYDITKMPECYFYS
          P.M....VAVCTFFLKGFCEKGQLCPF.HDDG.KTVVCKHWLRGLCKKSDH.KFLHQYDITKMPECYFYS
Retrocopy PLMLLTPVAVCTFFLKGFCEKGQLCPFQHDDGAKTVVCKHWLRGLCKKSDHSKFLHQYDITKMPECYFYS

Parental  KFGECSNKECLFLHADPAFKIRDCPWYDQGFCKYGLLCKFRHTRRVLCTNYLVGFCPEGPDCKFT
          KFGECSNKECLFLHADPAFKIRDCPWYDQGFCKY.LLCKFRH.RR.LCT.YLVGFCPEG.D.KFT
Retrocopy KFGECSNKECLFLHADPAFKIRDCPWYDQGFCKYSLLCKFRHNRRLLCTSYLVGFCPEGHDYKFT

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	0.24 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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_558 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_558 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019911	1 retrocopy	retro_cjac_2207,
Myotis lucifugus	ENSMLUG00000009617	2 retrocopies	retro_mluc_1935, retro_mluc_1936,
Monodelphis domestica	ENSMODG00000025672	1 retrocopy	retro_mdom_558 ,