RetrogeneDB ID: retro_mdom_1131

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:198236239..198236919(-)
• Located in intron of: ENSMODG00000028160

Retrocopy information

• Ensembl ID: ENSMODG00000010803
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSMODG00000011310
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_mdom_1131
CCCTCAGTCTTGGACAGCTTTGCTCTACTCTCTGGACAGCTGAATACCCTCAACAAAGTCCTCAAGCATGAGAAGACCCC
ATTGCTCCGAAATCAGGTCATCATTCCTTTGGTACTGTCCCCGGATCGTGATGAGGCGCTCACGCGGCAGACAGAGGGAC
AAGTTCCCGTCTTCAGTCATGAGGTGGTTCCTGATCACCTGAGAACCAAACCAGACCCGGAAGTGGAAGAACAAGAGAAG
CAGCTGACCGCAGATGCTGCTCGAATTGGCACTGACGCAGCCCAGAAGCAAATTCAGACTTTGAATAAAATGTGCTCCAA
TCTACTGGAGAAAATCAGCAAAGAGGAGCGGGAATCAGAAAGTGGAGGTCTCCGTCAGAACAAGCAGACCTTTAACCCCA
CAGACACCAACGCCCTGGTGGCTGCAGTTGCCTTTGGCAAGGGTCTATCCAACTGGAGGCCTCCAGGCAGCAGTGGACCT
GGCCAACCAGGCCAACCTGGGGCAGGGGCCCTCCTGGACGTTCATCGGGCATTCAGCAAGTTCAGATGACAGGGACACCC
AGTCAGCAACAGAGCACTCTGCTCAGCGGGGTTCAGATGGCGCAAACTGGCCAGCCAGGTAAGATGCCAAGCGGCATAAA
AACCAACATCAAGTCAGCTTCGATGCACCCCTACCAACGA

Alignment

ORF - retro_mdom_1131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 84.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSVLDSFALLSGQLNTLNKVLKHEKTPLLRNQVIIPLVLSPDRDEELTRQTEGRVPVFSHEVVPDHLRTK
          PSVLDSFALLSGQLNTLNKVLKHEKTPLLRNQVIIPLVLSPDRDE.LTRQTEG.VPVFSHEVVPDHLRTK
Retrocopy PSVLDSFALLSGQLNTLNKVLKHEKTPLLRNQVIIPLVLSPDRDEALTRQTEGQVPVFSHEVVPDHLRTK

Parental  PDPEVEEQEKQLTADAARIGTDAAQKQIQTLNKMCSNLLEKISKEERESESGGLRQNKQTFNPTDTNALV
          PDPEVEEQEKQLTADAARIGTDAAQKQIQTLNKMCSNLLEKISKEERESESGGLRQNKQTFNPTDTNALV
Retrocopy PDPEVEEQEKQLTADAARIGTDAAQKQIQTLNKMCSNLLEKISKEERESESGGLRQNKQTFNPTDTNALV

Parental  AAVAFGKGLSNWRPPGSSGPGQPGQPGAGALLD-SSGIQQVQMTGTPSQQQSTLLSG-VQMAQTGQPGKM
          AAVAFGKGLSNWRPPGSS.........AGALLD...........G.P.........G.VQMAQTGQPGKM
Retrocopy AAVAFGKGLSNWRPPGSSXXXXXXXXXAGALLDVHRAFSKFR*QGHPVSNRALCSAG<VQMAQTGQPGKM

Parental  PSGIKTNIKSASMHPYQR
          PSGIKTNIKSASMHPYQR
Retrocopy PSGIKTNIKSASMHPYQR

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_1131 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1131 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Erinaceus europaeus	ENSEEUG00000002286	1 retrocopy	retro_eeur_117,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131 ,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,