RetrogeneDB ID: retro_mdom_58

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:190159241..190160108(+)
• Located in intron of: ENSMODG00000016213

Retrocopy information

• Ensembl ID: ENSMODG00000024817
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013151
• Aliases: None
• Description: None

Sequence

>retro_mdom_58
AAGATGGCGGCAGCGGCGGTTCCCGGAGTGAACGGCTCCGGTGCAGCCAACGCTTCTGGAGGCTCTGGGGCGGTGCTTCA
GACAGCCGCCCTCATGTACGAGCAGCTCAAGGGCGAGTGGAACCGCAAGAGTCCCAATCTGAGCAGGTGCGGCGAGGAAC
TGGGCCGCCTCAAGTTGGTGCTGCTGGATCTCAACTTCCTGCCCACCACGGGGACAAAGCTGACGAAGCAGCAGCTCATC
CTGGCCCGGGACATCCTAGAGATTGGGGCCCAGTGGAGCATCCTGCGCAAGGACATCCCCTCCTTCGAGCGCTATATGGC
CCAGCTCAAGTGCTACTACTTTGACTACAAGGAGCAGCTCCCTGAGTCGGCCTACATGCACCAGCTCCTGGGCCTCAACC
TGCTCTTCCTGCTGTCCCAAAACCGAGTGGCCGAGTTCCACACGGAGCTGGAACGGCTGCCCGCCAAGGACATCCAGACT
AACGTCTACATCAAGCACCCCGTGTCTTTGGAGCAGTACCTGATGGAAGGAAGCTACAACAAAGTGTTCCTGGCCAAAGG
CAACATCCCAGCCGAGAGCTACACCTTCTTCATCGACATTTTGCTGGACACCATCAGGGACGAGATCGCGGGTTGTATTG
AGAAAGCCTATGAAAAGATTCTGTTTGCTGAAGCCACTCGCATCCTCTTCTTCACCAACCCCAAGAAGATGACTGAGTAT
GCCAAGAAGAGAGGATGGTGCCTGGGCCCCAACAATTACTACAGTTTCAAGTGTCAGCAGCCAAAGCCGGAGGACACAAC
CATCCCCTCCACTGAGCTGGCCAAGCAAGTCATTGAGTATGCCAGGCAGCTGGAGATGATTGTCTAA

Alignment

ORF - retro_mdom_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 97.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMAAAA---VNGAAGASTTGGSGAMLQAAAVMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT
          KMAAAA...VNG...A...GGSGA.LQ.AA.MYEQLKGEWNRKSPNLS.CGEELGRLKLVLL.LNFLPTT
Retrocopy KMAAAAVPGVNGSGAANASGGSGAVLQTAALMYEQLKGEWNRKSPNLSRCGEELGRLKLVLLDLNFLPTT

Parental  GTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQ
          GTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQ
Retrocopy GTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQ

Parental  NRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA
          NRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA
Retrocopy NRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA

Parental  GCIEKAYEKILFAEATRILFFTTPKKMTEYAKKRGWVLGPSNYYSFKCQQQKPEDTTIPSTELAKQVIEY
          GCIEKAYEKILFAEATRILFFT.PKKMTEYAKKRGW.LGP.NYYSFKCQQ.KPEDTTIPSTELAKQVIEY
Retrocopy GCIEKAYEKILFAEATRILFFTNPKKMTEYAKKRGWCLGPNNYYSFKCQQPKPEDTTIPSTELAKQVIEY

Parental  ARQLEMIV
          ARQLEMIV
Retrocopy ARQLEMIV

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_58 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_58 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005931	1 retrocopy	retro_cfam_2206,
Echinops telfairi	ENSETEG00000013316	3 retrocopies	retro_etel_1148, retro_etel_1902, retro_etel_285,
Homo sapiens	ENSG00000099341	1 retrocopy	retro_hsap_456,
Macropus eugenii	ENSMEUG00000006596	2 retrocopies	retro_meug_1494, retro_meug_173,
Myotis lucifugus	ENSMLUG00000009902	2 retrocopies	retro_mluc_2137, retro_mluc_2480,
Macaca mulatta	ENSMMUG00000031219	1 retrocopy	retro_mmul_534,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58 ,
Nomascus leucogenys	ENSNLEG00000016876	1 retrocopy	retro_nleu_878,
Otolemur garnettii	ENSOGAG00000004068	1 retrocopy	retro_ogar_1338,
Pongo abelii	ENSPPYG00000009931	1 retrocopy	retro_pabe_277,
Pan troglodytes	ENSPTRG00000010926	1 retrocopy	retro_ptro_343,
Sus scrofa	ENSSSCG00000002956	1 retrocopy	retro_sscr_195,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,