RetrogeneDB ID: retro_mdom_745

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:303727729..303728122(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018789
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013730
• Aliases: None
• Description: Ferritin [Source:UniProtKB/TrEMBL;Acc:F6XQK5]

Sequence

>retro_mdom_745
GTCGCTCTGTCCAAGATGTCGAGCTTTTTCCGGGAACTGTCCCGGGAGAAGCGCGAAGCCGCTGAGTGCCTCCTCCGCCT
CCAGAACCAACATGGAGGCCGTGTGCACCTACAAGCTGTGGTGAAACCTGCCCAAGACGAGTGGGGCGGCAGCAGAGATG
CCATTGAGTCCGCCCTCAACCTGGAAAAGGGCCTGAACCAGACCTTCCTGAAACTGCACGCCCTGGCTTCCAGCCAGGGG
GATCCTCACCTCTGCGACTTCCTGGAAAGCCACTACCTGGAGGAGGAGACGAAGCTGCTGAAGCGTCTGGGAGACCACCT
GACCTCCCTGGGCCATGTGCAAAGCCCGGGCGGCCTGGGCGAGTACCTGTTCGAGAGACTGACCCTGAATGAC

Alignment

ORF - retro_mdom_745 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 58.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VALAKMSSFFRELSREKREAAERLLRLQNQRGGRVHLQAVVKPAQDEWGGSRDAIESALNLEKGLNQTLL
          VAL.KMSSFFRELSREKREAAE.LLRLQNQ.GGRVHLQAVVKPAQDEWGGSRDAIESALNLEKGLNQT.L
Retrocopy VALSKMSSFFRELSREKREAAECLLRLQNQHGGRVHLQAVVKPAQDEWGGSRDAIESALNLEKGLNQTFL

Parental  KLHALASSQGDPHLCDFLESHYLEEEAKLLKRLGDHLTSLGHVQSQGGLGEYLFERLSLND
          KLHALASSQGDPHLCDFLESHYLEEE.KLLKRLGDHLTSLGHVQS.GGLGEYLFERL.LND
Retrocopy KLHALASSQGDPHLCDFLESHYLEEETKLLKRLGDHLTSLGHVQSPGGLGEYLFERLTLND

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_745 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_745 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 5 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006157	5 retrocopies	retro_meug_1020, retro_meug_1224, retro_meug_1314, retro_meug_1425, retro_meug_349,
Monodelphis domestica	ENSMODG00000001863	5 retrocopies	retro_mdom_1250, retro_mdom_302, retro_mdom_551, retro_mdom_789, retro_mdom_848,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Monodelphis domestica	ENSMODG00000013730	3 retrocopies	retro_mdom_1989, retro_mdom_6, retro_mdom_745 ,
Sarcophilus harrisii	ENSSHAG00000003637	1 retrocopy	retro_shar_595,