RetrogeneDB ID: retro_itri_1098

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393375.1:6907564..6907951(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSSTOG00000002537
• Aliases: None
• Description: peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354]

Sequence

>retro_itri_1098
TATGCTCCCGCTGCCACCCAGCATGTGCCGGATTTTAAGGGGAGAGCTATTGCCTATGGAGAGTTCAAAGAACTAAGCCT
AGAGGACTTTGAAGGGAAATATTGATGCTTCCTTTTATCATTTGGCTTTCACCTTTGTGGGTTCTTCAGAAATTATTGCT
TTTAGAGACAAAGACAAAGAACAATCATGATGTTAACTGTGAACTTGTTGTTGTTTGGTGGGTTTCTATTTAAACCATGT
TGCCTGAATAAACACATCAGAGAAGAGAGGCAGATTGGACCACAAGAGTTTGCACCCTTGTCAGAGTTAACAAAACAGAT
CTCCTGAGGCCAAGGTGTGCTGCTAGGAGGTTTTGGTCTCATACTAACAGAGTTGTTCCTACATGAT

Alignment

ORF - retro_itri_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.78 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HAPAVTQHAPYFKGTAVVNGEFKELNLDDFKGKY-LVLFF-YPLDFTFVCPTEIIAFSDKANE-FHDVNC
          .APA.TQH.P.FKG.A...GEFKEL.L.DF.GKY.L.L.F.Y.L.FTFV...EIIAF.DK..E..HDVNC
Retrocopy YAPAATQHVPDFKGRAIAYGEFKELSLEDFEGKY<LMLPF<YHLAFTFVGSSEIIAFRDKDKE>NHDVNC

Parental  EVVAV-SVDSHFTHLAWINTPRKNGGLGHMNI-ALLSDLTKQISRDYGVLLEGAGLALRGLFIID
          E.V.V..V.....H.A.INT..K.G.L.H....A.LS.LTKQIS...GVLL.G.GL.L..LF..D
Retrocopy ELVVV<LVGFYLNHVA*INTSEKRGRLDHKSL<APLSELTKQIS*GQGVLLGGFGLILTELFLHD

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_1098 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1098 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 25 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Mus musculus	ENSMUSG00000024997	1 retrocopy	retro_mmus_2443,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098 , retro_itri_1753,
Ictidomys tridecemlineatus	ENSSTOG00000023413	2 retrocopies	retro_itri_631, retro_itri_817,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,