RetrogeneDB ID: retro_mdom_1774

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:53810676..53810950(-)
• Located in intron of: ENSMODG00000000682

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSMODG00000017579
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_mdom_1774
GTAAGAGAACCATTATCTAATTCTAAGGAACAATGTTCTTTCATCAAGTATAAACATTTTAAGCTGATATACTGGCAGTA
CGTAACTATTTTTACCATGGTTAGAATCAATAAAGCTGACAATGAAATGGATATATATGAATCCATCCATAACTTTTCAA
AGTTTCAGACAAGGGTTTCAGCCAAGTGCCTGAATAAGATACAATGATTAACTTGGATCAAGTACATATCATTTGGATCA
AACAGTGCTGCATAATTGTATGGTAAAAACTAAC

Alignment

ORF - retro_mdom_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IKTCLTRSKEQCSFIEYKDFKLIYRQYAALFIVVGINDTENEMAVYEFIHNF-VEVLDMYFSRVSELDIM
          ....L..SKEQCSFI.YK.FKLIY.QY...F..V.IN...NEM..YE.IHNF...V.D..FS.V.E.D.M
Retrocopy VREPLSNSKEQCSFIKYKHFKLIYWQYVTIFTMVRINKADNEMDIYESIHNF<FKVSDKGFSQVPE*DTM

Parental  FNLDKVHII-LDEMVLNGCIVETN
          .NLD.VHII.LD..VL..C.V.TN
Retrocopy INLDQVHII<LDQTVLHNCMVKTN

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	20.03 RPM
SRP007412_cerebellum	0.00 RPM	29.71 RPM
SRP007412_heart	0.00 RPM	23.52 RPM
SRP007412_kidney	0.00 RPM	38.19 RPM
SRP007412_liver	0.00 RPM	36.25 RPM
SRP007412_testis	0.00 RPM	8.25 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1774 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1774 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 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Callithrix jacchus	ENSCJAG00000005786	1 retrocopy	retro_cjac_2742,
Dipodomys ordii	ENSDORG00000009468	1 retrocopy	retro_dord_595,
Erinaceus europaeus	ENSEEUG00000013009	1 retrocopy	retro_eeur_301,
Homo sapiens	ENSG00000100478	1 retrocopy	retro_hsap_3496,
Gorilla gorilla	ENSGGOG00000003198	1 retrocopy	retro_ggor_2363,
Myotis lucifugus	ENSMLUG00000011671	1 retrocopy	retro_mluc_1841,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774 ,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Nomascus leucogenys	ENSNLEG00000015901	1 retrocopy	retro_nleu_788,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,
Pan troglodytes	ENSPTRG00000006239	1 retrocopy	retro_ptro_2368,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Rattus norvegicus	ENSRNOG00000005765	1 retrocopy	retro_rnor_2200,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,