RetrogeneDB ID: retro_sara_164

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_5365:74413..74646(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA52
• Ensembl ID: ENSSARG00000000984
• Aliases: None
• Description: ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:HGNC Symbol;Acc:12458]

Sequence

>retro_sara_164
AGAAGACTTACTCTCAAGGCTGAATCATTAGATACAATAGAAAATATAGAGGCCAAGGTTCAGGATAAGAAAGGAATTCC
TCCAGGTCAGCAAAGAATGATCTTTGCTGGTAAATGACTTGAAGCTGGACATACTTTGTCTGATACAACATCCAAAAGGA
GTCCATTCTTCATCTTGTTTTCAGACTTAGGGGCAGAAGTCTTACTCTACTCCACAGAAGAATAAGCAGAAGA

Alignment

ORF - retro_sara_164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.76 %
• Parental protein coverage: 60.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD-YNIQKESTLHLVLRLRGGIIE
          ...TL..E..DTIEN..AK.QDK.GIPP.QQR.IFAGK.LE.G.TLSD.YNIQKES.LHLV.RLRG....
Retrocopy RRLTLKAESLDTIENIEAKVQDKKGIPPGQQRMIFAGK*LEAGHTLSD<YNIQKESILHLVFRLRGRSLT

Parental  PSLRQLAQK
          ...R.....
Retrocopy LLHRRISRR

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_164 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011356	10 retrocopies	retro_amel_1045, retro_amel_1416, retro_amel_1455, retro_amel_1759, retro_amel_1849, retro_amel_214, retro_amel_800, retro_amel_904, retro_amel_941, retro_amel_973,
Callithrix jacchus	ENSCJAG00000007470	22 retrocopies	retro_cjac_1363, retro_cjac_1388, retro_cjac_1426, retro_cjac_1485, retro_cjac_1521, retro_cjac_1561, retro_cjac_1731, retro_cjac_1743, retro_cjac_2002, retro_cjac_207, retro_cjac_2254, retro_cjac_2292, retro_cjac_2413, retro_cjac_2501, retro_cjac_2505, retro_cjac_2898, retro_cjac_3054, retro_cjac_658, retro_cjac_683, retro_cjac_883, retro_cjac_892, retro_cjac_898,
Cavia porcellus	ENSCPOG00000000351	3 retrocopies	retro_cpor_1454, retro_cpor_1471, retro_cpor_1502,
Equus caballus	ENSECAG00000020660	8 retrocopies	retro_ecab_1014, retro_ecab_107, retro_ecab_313, retro_ecab_641, retro_ecab_772, retro_ecab_835, retro_ecab_836, retro_ecab_857,
Felis catus	ENSFCAG00000009745	14 retrocopies	retro_fcat_1159, retro_fcat_1204, retro_fcat_1226, retro_fcat_1232, retro_fcat_1382, retro_fcat_1428, retro_fcat_1449, retro_fcat_1540, retro_fcat_1661, retro_fcat_86, retro_fcat_876, retro_fcat_909, retro_fcat_939, retro_fcat_989,
Gorilla gorilla	ENSGGOG00000004630	8 retrocopies	retro_ggor_1021, retro_ggor_1045, retro_ggor_1265, retro_ggor_1835, retro_ggor_2579, retro_ggor_2687, retro_ggor_2782, retro_ggor_905,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Myotis lucifugus	ENSMLUG00000029594	5 retrocopies	retro_mluc_1995, retro_mluc_2057, retro_mluc_2203, retro_mluc_44, retro_mluc_829,
Macaca mulatta	ENSMMUG00000016085	7 retrocopies	retro_mmul_1184, retro_mmul_1580, retro_mmul_1625, retro_mmul_2183, retro_mmul_2311, retro_mmul_232, retro_mmul_896,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Sorex araneus	ENSSARG00000000984	11 retrocopies	retro_sara_145, retro_sara_164 , retro_sara_192, retro_sara_256, retro_sara_281, retro_sara_331, retro_sara_344, retro_sara_599, retro_sara_67, retro_sara_687, retro_sara_94,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,