RetrogeneDB ID: retro_mdom_1881

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:213266121..213266629(+)
• Located in intron of: ENSMODG00000001864

Retrocopy information

• Ensembl ID: ENSMODG00000001869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSMODG00000025788
• Aliases: None
• Description: AKT interacting protein [Source:HGNC Symbol;Acc:16710]

Sequence

>retro_mdom_1881
ACAGTTTATATCCCTGATAACTATCTAGATGGTGATTGTCCATGTTTGGTGTTTGATATCCCTGTCTTCCACCCACTAGT
TGATCCCATCTCAGGTGAACTGGATGTGAAGAGAGCATTTGCAAAATGGAGGATGAACCATAATCACATCTGGCAAGTGT
TGATGTATGCACGACGAGTTTTCTACAAGATTGATACAACTACCCCCTTTGAACCCAGAGGCTACAGTATTGTATGAAAA
GTATGTTCAACTTTTTGAAAGTAAAGTGGTTGACAGTGTCCAATTATGCACCACCCATTTGTTTGACCAGCCTAAAATAG
AAGATCCCTATGCAATTAGTTTTTCTCCATGGAATCCCTCTATACATGATGATGCTAGACAGAAGATGCTGACTCAGAAA
AAGAAACCAGAAGAACAGCATAGTAAAAACCTCCACATCACTGGTCTGTCATGGGTAAAGCCTGGCTCAGTGCAACCTTT
CAGTATAGAGGAGAAAACAGTAACAACT

Alignment

ORF - retro_mdom_1881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVYIPDNYPDGDCPRLVFDIPVFHPLVDPISGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKIDTTT-P
          TVYIPDNY.DGDCP.LVFDIPVFHPLVDPISGELDVKRAFAKWR.NHNHIWQVLMYARRVFYKIDTTT.P
Retrocopy TVYIPDNYLDGDCPCLVFDIPVFHPLVDPISGELDVKRAFAKWRMNHNHIWQVLMYARRVFYKIDTTT>P

Parental  LNPEAAVLYEKDVQLFKSKVVDSVQLCTTHLFDQPKIEDPYAISFSPWNPSIHDDAREKMLTQ-KKPEEQ
          LNPEA.VLYEK.VQLF.SKVVDSVQLCTTHLFDQPKIEDPYAISFSPWNPSIHDDAR.KMLTQ.KKPEEQ
Retrocopy LNPEATVLYEKYVQLFESKVVDSVQLCTTHLFDQPKIEDPYAISFSPWNPSIHDDARQKMLTQKKKPEEQ

Parental  HSKNLHVAGLSWVKPGSVQPFSKEEKTVTT
          HSKNLH..GLSWVKPGSVQPFS.EEKTVTT
Retrocopy HSKNLHITGLSWVKPGSVQPFSIEEKTVTT

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	368.68 RPM
SRP007412_cerebellum	0.00 RPM	318.29 RPM
SRP007412_heart	0.00 RPM	232.84 RPM
SRP007412_kidney	0.00 RPM	293.65 RPM
SRP007412_liver	0.00 RPM	125.87 RPM
SRP007412_testis	0.00 RPM	1092.96 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1881 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1881 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533, retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881 ,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,