RetrogeneDB ID: retro_mdom_244

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:669175596..669176244(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023076
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016618
• Aliases: None
• Description: None

Sequence

>retro_mdom_244
ATGAGCTGCACAATTGAAAAAGCTCTTGCAGATGCTAAAGCACTTGTTGAACGATTAAGAGACCATGACAATGCAGCAGA
ATCTCTGATTGAACAAACTACGGCTCTCAACAAGCGAGTGGCAGCAATGAAACAGTATCAAGAAGAAATTCAAGAACTTA
ATGAGGTTGCAAGACACCGACCACGATCTACATTAGTTATGGGAATTCAGCAAGAAAACAGGCAAATCAGAGAATTGCAG
CAAGAAAATAAAGAATTACGCACATCGCTTGAGGAACACCAGTCTGCTTTAGAACTCATAATGAGCAAGTACCGAGAGCA
AATGTTTAGGTTGTTAATGGCCAGCAAAAAGGATGACCCAGGTATTATAATGAAGTTAAAGGAGCAACATTCCAAGGAAT
TACAAGTACATGTGGACCAGATTACTGAAATGGCAGCAGTAATGAGGAAAGCTATTGAAATTGATGAGCAGCAAGGTTGT
AAGGAGCAGGAACGGATTTTTCAACTTGAACAAGAAAACAAGGGCTTGAGAGAAATCCTCCAAATAACTCGAGAATCATT
CCTGAGCCTCAAAAAAGATGATGCATCAGAGAGTACATCTTTGTCAGCATTGGTAACCAACAGTGATTTGAGCCTGAGAA
AGAGCTGA

Alignment

ORF - retro_mdom_244 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 53.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHDNAAESLIEQTTALNKRVEAMKQYQEEIQELNEVARHRPRSTLVMGIQ
          MSCTIEKALADAKALVERLRDHDNAAESLIEQTTALNKRV.AMKQYQEEIQELNEVARHRPRSTLVMGIQ
Retrocopy MSCTIEKALADAKALVERLRDHDNAAESLIEQTTALNKRVAAMKQYQEEIQELNEVARHRPRSTLVMGIQ

Parental  QENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKIDMVH
          QENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSK...VH
Retrocopy QENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKELQVH

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	3.46 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	18.07 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_244 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_244 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244 ,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,