RetrogeneDB ID: retro_dord_175

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4523:50264..50652(+)
• Located in intron of: ENSDORG00000005150

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl32
• Ensembl ID: ENSDORG00000008426
• Aliases: None
• Description: ribosomal protein L32 [Source:MGI Symbol;Acc:MGI:98038]

Sequence

>retro_dord_175
AAACCTCCTGTGAAGCCCTAGATTGTTCACACAATGACCAACAAATTCACTCATCACAGATCAATCTAATATGTCAAAAT
TAAATGTAAGTGGCAGAAATACTCAAGTATCGACAAGAAGATATGGAGAAGACTCAAGAGCCATATTTGGATGCTCAACA
CTGGTTACAGGAACAACAAGAAAAGGAAAACTATCCTTCCCATTGGCTGCAGAAGTGTCTGGGTCACAGTATCACAGAGC
TGGAACCACTGATGATGTGCAATAAATTTTACTGTGCTGAGATTGCTCACAATGCTTCCTCTAAGAACCACAAAGCCATC
ATGGAAAGAGCAGCTTAGCTAGCCATCAGATCACTGATACTAATGCCAGAATCCCCAGCAAAGAAAAT

Alignment

ORF - retro_dord_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 96.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLPSGF
          .P.VKP.IV...T.KF..H.S..YVKIK..W.K...ID....RR.K..I.M.N.GY..NKK.K..LP.G.
Retrocopy KPPVKP*IVHTMTNKFTHHRSI*YVKIKCKWQKYSSIDKKIWRRLKSHIWMLNTGYRNNKKRKTILPIGC

Parental  R-KFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIR-VTNPNARLRSEEN
          R.K.L.H...ELE.L.MCNK.YCAEIAHN.SSKN.KAI.ERAA.LAIR..T..NAR..S.EN
Retrocopy R<KCLGHSITELEPLMMCNKFYCAEIAHNASSKNHKAIMERAA*LAIR<ITDTNARIPSKEN

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_175 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 92 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,
Dipodomys ordii	ENSDORG00000008426	6 retrocopies	retro_dord_175 , retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
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,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,