RetrogeneDB ID: retro_itri_1294

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393429.1:2879241..2879591(-)
• Located in intron of: ENSSTOG00000012406

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSSTOG00000026505
• Aliases: None
• Description: ribosomal protein L32 [Source:HGNC Symbol;Acc:10336]

Sequence

>retro_itri_1294
ATGGCTTCCCTCAGACCTCTGGTGAAACCCAAAATTGTCAAAAAGAGGACCAAGAAGTTCATCTGGCACCTGGTAAGACT
AATATGCCAAAATTAAGCACAACTGGTAGAAACCCAGAGATACTGACAAAAGGGTATAGAGAAGATTAAGGGCTAGATCC
TTATGACAAACATTGGTATGAGAGCAGCAGGAGAACAAAGCATATGTTGCCCAGAGGCCTCCAGAAGTTCCTGATCCCCA
TTATCAAGGAGCTGGAAGTGCTGCTAATGTGCAACAAACCTTCCTGTACTATGACTGCTCACCATGTTTCCTTCAAGAAC
CTTAAAGTCAGCATGGAACAGCCCAGCAGG

Alignment

ORF - retro_itri_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQS-DRYVKIKRNWRKPRGIDNRVRRRF-KGQILMPNIG-YGSNKKTK
          MA.LRPLVKPKIVKKRTKKFI.H...D.Y.KIK.NW.KPR..D.RV.RR..KG.ILM.NIG.Y.S...TK
Retrocopy MASLRPLVKPKIVKKRTKKFIWHLV>D*YAKIKHNW*KPRDTDKRV*RRL<KG*ILMTNIG<YESSRRTK

Parental  HMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQ
          HMLP.G..KFL....KELEVLLMCNK..C...AH.VS.KN.K...E....
Retrocopy HMLPRGLQKFLIPIIKELEVLLMCNKPSCTMTAHHVSFKNLKVSMEQPSR

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_1294 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1294 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 12 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Cavia porcellus	ENSCPOG00000019967	2 retrocopies	retro_cpor_1241, retro_cpor_608,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus	ENSEEUG00000011609	5 retrocopies	retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39, retro_eeur_576,
Homo sapiens	ENSG00000144713	20 retrocopies	retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024, retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677, retro_hsap_814,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Ictidomys tridecemlineatus	ENSSTOG00000026505	9 retrocopies	retro_itri_1294 , retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,