RetrogeneDB ID: retro_itri_312

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:18816667..18817328(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023565
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSSTOG00000003783
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 [Source:HGNC Symbol;Acc:9555]

Sequence

>retro_itri_312
TGTGTGTCTAACTGGTTGGTCTGCAACCCCGCCTACAGTGAGAAGCTGGAGGAGTTAAAGGAGCACATCCTGGCCTATAA
ATCACTGGCTACTAGAACTGACCAGGACAGCAGAACCGCATTGCACTGGGCATGTTCAGCAGGACATACTGAAATTGTTG
AGTTCTTGCTACATCTTGGAGTGCCAGTGAATGATAAAGATGATGCAGGCCTGTCTCCTCTAAATATTGCAGCTTCTGCT
GGCCGGGATGAAATCGTAAAAGCGCTCCTGGGAAAAGGTGGGCATGTGAATGCTGTCAATCAAAATGGCTGTATTCCCCT
ACACTGTGCTGCTTCCAAAAACAGGCGTGAGATTGCTGCCGTGTTCCTACAAGGTGAGCCTAATCCAGATGCTCATTATG
AGGCTACGGCAACGCACCAGGGTAAAGCAGCCAAGGGTAACCTGAAGATGATTCATAGCCTTCTGTACTACAAAGCATCC
ACAGACATCCAAGACACTGGAGGGTAACACTCCTCTACACTTAGCCTGTGAGAGAGTAGAAGCAGCAAAGCTGCGAGGGT
CCCAGGGAGCAAGTGTATACATTGAGAATGAGGAAGAAAAGACACCACTGCAAGGGGCCAGAGGTGGCCTGGGTTTAATA
CTCAAGACAATGGTTGAAGGG

Alignment

ORF - retro_itri_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.67 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVSNLMVCNLAYSGKLEELKESILADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDKDDAG
          CVSN..VCN.AYS.KLEELKE.ILA.KSLATRTDQDSRTALHWACSAGHTEIVEFLL.LGVPVNDKDDAG
Retrocopy CVSNWLVCNPAYSEKLEELKEHILAYKSLATRTDQDSRTALHWACSAGHTEIVEFLLHLGVPVNDKDDAG

Parental  WSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYEATAM
          .SPL.IAASAGRDEIVKALLGKG..VNAVNQNGC.PLH.AASKNR.EIA...L.G..NPDA..HYEATA.
Retrocopy LSPLNIAASAGRDEIVKALLGKGGHVNAVNQNGCIPLHCAASKNRREIAAVFLQGEPNPDA--HYEATAT

Parental  HRA-AAKGNLKMIHILLYYKASTNIQDT-EGNTPLHLACDEERVEEAKLLVSQGASIYIENKEEKTPLQV
          H...AAKGNLKMIH.LLYYKAST.IQDT.EGNTPLHLAC..ERVE.AKL..SQGAS.YIEN.EEKTPLQ.
Retrocopy HQGKAAKGNLKMIHSLLYYKASTDIQDT>EGNTPLHLAC--ERVEAAKLRGSQGASVYIENEEEKTPLQG

Parental  AKGGLGLILKRMVEG
          A.GGLGLILK.MVEG
Retrocopy ARGGLGLILKTMVEG

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_312 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_312 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 15 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312 , retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,