RetrogeneDB ID: retro_mdom_228

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:77806119..77806842(-)
• Located in intron of: ENSMODG00000000176

Retrocopy information

• Ensembl ID: ENSMODG00000000179
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020396
• Aliases: None
• Description: None

Sequence

>retro_mdom_228
TTAAAAATGGGAGTTGTCAGTGGATTTATAAAATATTCTATGTTTGTCTTCAACTTCATATTCTGGGTATGTGGCAGCAT
AATCCTGGGAATAGCAATATATGCACGTACCAGCAAAATCGGTCAAGAGATCATTCGTGGAGAAGCATCTGGAATGAATA
CACGTACAGCTGCAAATCTCTTGATAGCTGTGGGTACCATTATCATGGTCCTCGGTTTCCTGGGATGCTGTGGTGCTTTG
AAGGAAAATCGTTGCATGCTGCTCTTGTTTTTCGTTGGATTACTTGTGATTGTGATTATTCAGATTGTAGTAGGTGTGGT
AGGACTGTCCTTCAAAACTAAGATTGAAAAAGCTTTTAAAAAGAGTTTTGAGCATGAAGTGATGACTTTGAGCAAAGATG
ATCCTCAGTCTCAGACATTTCAAAAGAACTTGGAGAAAATGCAAGAGAAGTTTAAGTGCTGTGGCTTGATCAGAGGAGCA
GCTGACTGGGGAAAGAACTTCAACAAGTATGGTGGATCATGTGAATGTACAAGTTCTGTACTTAATGATTGTGTAGACTA
TCCGGGAAAACATGTTTACAGAGAGTCATGTGGTCAGCATATTATTAATTACCTGAAGAAAAATATGGTGATTGTTGCTG
GGGTTGCATTTGGAGTGGCAGTGATTGAGATACTTGGCCTGATCTTTTCTTATGTTTTATGGCGCCAGATTGGTCCAAAC
TAA

Alignment

ORF - retro_mdom_228 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVVSGFIKYSMFVFNFIFWVCGSIILGIAIYARTSKIGQEIIRGEASGMNTHTAANLLIAVGTIIMVLG
          MGVVSGFIKYSMFVFNFIFWVCGSIILGIAIYARTSKIGQEIIRGEASGMNT.TAANLLIAVGTIIMVLG
Retrocopy MGVVSGFIKYSMFVFNFIFWVCGSIILGIAIYARTSKIGQEIIRGEASGMNTRTAANLLIAVGTIIMVLG

Parental  FLGCCGALKENRCMLLLFFVGLLVIVIIQIVAGVVGLSFKTKIEKAFKKSFEHEVMTLSKDDPQSQTFQK
          FLGCCGALKENRCMLLLFFVGLLVIVIIQIV.GVVGLSFKTKIEKAFKKSFEHEVMTLSKDDPQSQTFQK
Retrocopy FLGCCGALKENRCMLLLFFVGLLVIVIIQIVVGVVGLSFKTKIEKAFKKSFEHEVMTLSKDDPQSQTFQK

Parental  NLEKMQKKFKCCGLIRGAADWGKNFDKYGGSCECTSSVLNDCVDYQGKHVYRESCGQHIINYLKKNMVIV
          NLEKMQ.KFKCCGLIRGAADWGKNF.KYGGSCECTSSVLNDCVDY.GKHVYRESCGQHIINYLKKNMVIV
Retrocopy NLEKMQEKFKCCGLIRGAADWGKNFNKYGGSCECTSSVLNDCVDYPGKHVYRESCGQHIINYLKKNMVIV

Parental  AGVAFGVAVVEILGLIFSYVLWRQIGAN
          AGVAFGVAV.EILGLIFSYVLWRQIG.N
Retrocopy AGVAFGVAVIEILGLIFSYVLWRQIGPN

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_228 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_228 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
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490, retro_mdom_226, retro_mdom_872,
Monodelphis domestica	ENSMODG00000020396	1 retrocopy	retro_mdom_228 ,
Sarcophilus harrisii	ENSSHAG00000007931	1 retrocopy	retro_shar_368,