RetrogeneDB ID: retro_mdom_1788

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:110015044..110015544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1788
AAACAGGCAAATCAGAGAATTGCAGCAAGAAAATAATTACACACATCGCTTGAGAAACACCAATCTGCTTTAGAACTCAG
AATGAGCAAGTGCCAAAAGCAAATGTTTAGGTTCTTAAGGACCAGCAAAAAAGGATGACGCAGGTATTATAATGAAGTTA
AAGGAGCAACAGTCCAAGATTGACATGGTACACCGTCATCACAGCCCTGAAGGAATCTTCTTGGTGCACCTCGACACCTC
CTTGAAGCAACTCTACACGGACTGGAGAGAAGGCACTTGGAAGCCAATCTGAATCATTACAAGTACATGTGGACCAGATT
ACTGAAAGGGCTGCAGTAATGAGGAAAGCTTTTGAAATTGATGAGCAGCAAGGTTGTAAGGAGCAGGAACGAATTTTTCA
ACTTGAACAAGAAAACAAAGGCTTGAGGGAAATCCTCCAAATAACTTGAGAATCATTCCTGAGCCTCAAGAAAGATGATG
CATCAGAGAGTACATCGTTG

Alignment

ORF - retro_mdom_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKK-DDPGIIMKLKEQHSKIDMVHRHHSP
          .Q........K.L.TSLE.HQSALEL.MSK...QMFR.L..SKK.DD.GIIMKLKEQ.SKIDMVHRHHSP
Retrocopy KQANQRIAARK*LHTSLEKHQSALELRMSKCQKQMFRFLRTSKK>DDAGIIMKLKEQQSKIDMVHRHHSP

Parental  EGIFL-GAPRRILEATQHGLERRHLEANLNE-LQVHVDQITEMAAVMRKAIEIDEQQGCKEQERIFQLEQ
          EGIFL.GAPR..LEAT.HGLERRHLEANLN..LQVHVDQITE.AAVMRKA.EIDEQQGCKEQERIFQLEQ
Retrocopy EGIFL<GAPRHLLEATLHGLERRHLEANLNH<LQVHVDQITERAAVMRKAFEIDEQQGCKEQERIFQLEQ

Parental  ENKGLREILQITRESFLSLKKDDASESTSL
          ENKGLREILQIT.ESFLSLKKDDASESTSL
Retrocopy ENKGLREILQIT*ESFLSLKKDDASESTSL

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_1788 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1788 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,