RetrogeneDB ID: retro_itri_10

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393458.1:3813657..3814515(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027813
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSSTOG00000014464
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_itri_10
AAGATGGCGGTCAGCACGGCGAACAGGACGGCCCCTGCCGGCATCTGGAGCTCGGGGTCTGCAGTCCTGCAGGCGGCGGC
CGGCATGTACGAGCAACTCAAGGGCGAGTGGAACCGCAAGAGCCCCAATCTCAGCAAGTGCGGAGAAGAGCTGGGCCGCC
TCAAGCTGGTTCTGCTGGAGCTGAACTTCCTGCCCACCACGGGGACCAAGCTGACCAAACAACAGCTCATCCTGGCCCGT
GATATTTTGGAGATTGGGGCCCAGTGGAGCATCCTTCGCAAGAACATCCCCTCCTTCGAGCGCTACATGGCCCAGCTGAA
ATGCTACTACTTTGATTACAAGGGGCAGCTGCCCGAGTCCGCCTACATGCACCAGCTCCTGGGCCTCAACCTCCTCTTCC
TGCTGTCCCAGAACCGGGTGGCTGAGTTTCATACAGAGTTGGAGCGCCTCCCGGCCAAGGACATCCAGTCCAATGTCTAC
ATCAAGCACCCCGTGTCCATTGAGCAGTACCTGATGGAGGGTAGCTACAACAAGGTGTTCCTGGCCAAAGGTAACATCCC
TGCCGAGAGCTACACCTTCTTCATCGACATTCTGCTGGACACCATCAGGGATGAGATTGCAGGGTGCATTGAGAAGGCCT
ATGAGAAAATCCTTTTCAGTGAGGCCACCCGGATCCTCTTCTTCAACACACCCAGAAAGATGACGGAGTATGCTAAGAAG
CGAGGGTGGGTCCTGGGCCCCAACAGCTACTACAGTTTTTCCAGCCAGCAGCAGAAGCCAGAAGACACCACCATTCCCTC
CACGGAATTAGCCAAACAGGTCATGGAGTATGCTCGGCAGCTGGAGATGATTGTTTGA

Alignment

ORF - retro_itri_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.28 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMAAATMNGTTGISSSGSAAASGAILQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT
          KMA..T.N.T......G......A.LQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT
Retrocopy KMAVSTANRT---APAGIWSSGSAVLQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT

Parental  GTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQ
          GTKLTKQQLILARDILEIGAQWSILRK.IPSFERYMAQLKCYYFDYK.QLPESAYMHQLLGLNLLFLLSQ
Retrocopy GTKLTKQQLILARDILEIGAQWSILRKNIPSFERYMAQLKCYYFDYKGQLPESAYMHQLLGLNLLFLLSQ

Parental  NRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA
          NRVAEFHTELERLPAKDIQ.NVYIKHPVS.EQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA
Retrocopy NRVAEFHTELERLPAKDIQSNVYIKHPVSIEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIA

Parental  GCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRGWVLGPNNYYSFASQQQKPEDTIIPSTELAKQVIEY
          GCIEKAYEKILF.EATRILFFNTP.KMT.YAKKRGWVLGPN.YYSF.SQQQKPEDT.IPSTELAKQV.EY
Retrocopy GCIEKAYEKILFSEATRILFFNTPRKMTEYAKKRGWVLGPNSYYSFSSQQQKPEDTTIPSTELAKQVMEY

Parental  ARQLEMIV
          ARQLEMIV
Retrocopy ARQLEMIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_10 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_10 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 ,