RetrogeneDB ID: retro_sara_334

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_169325:476..910(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000012433
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000005798
• Aliases: None
• Description: None

Sequence

>retro_sara_334
ATGAAGTTCAACCCCTTCATCACTTGTTTGAGCAGCAAGTACCACAAACGCCCCTTCAAAGCCCCTTGCCCGTGCGTGGG
AAGATTATGTCATCACTGGTAAAGGAACGGCGGCAGAAATATAATATTGCTCCATGCTCATCCTAAAGGACACCGAGAGT
CCAGGTGGTTGGAGGACACTGCAAGGGTCAGCAACTCTGAAAGCTGGTTCAGGTTTACAAGAAAGAAATGCATCATCTGC
AAGCAGCGGGTGCAGCAGGAGATGGCCAACGACACGACGGTCCATGAGGGCGTTCAGACCAGCAAGGCGGTTATTACCAG
GCTAATATTGGACAAAGATTGAAAAAAAAATTGAGTGCAAAGTCAAATCTCGACAAATTGGAAAAGAGAAAGGCAAATAC
AAGGAAGAACTGTTTGAGAAAATGCAAGAATGAG

Alignment

ORF - retro_sara_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.95 %
• Parental protein coverage: 96.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSH-IRRKIMSSPLSKELRQKYNVR-SMPIRKDDE-VQVVRGHYKGQQI
          MKFNPF.T...SK..KR.F.AP....R.KIMSS.L.KE.RQKYN...SM.I.KD.E.VQVV.GH.KGQQ.
Retrocopy MKFNPFITCLSSKYHKRPFKAPCP<VRGKIMSS-LVKERRQKYNIA<SMLILKDTE>VQVVGGHCKGQQL

Parental  GKVVQVY-RKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDR-KKILERKAKSRQVGKEK-NI
          .K.VQVY.RKK..I...RVQ.E.AN.TTVH.G...SK.VITRL.LDKD.....L..K.......K.K.N.
Retrocopy *KLVQVY>RKKCIICKQRVQQEMANDTTVHEGVQTSKAVITRLILDKDX<XXXLSAKSNLDKLEKRKANT

Parental  RKKRLRRCRNK
          RK..LR.C.N.
Retrocopy RKNCLRKCKNE

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_334 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 130 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Sorex araneus	ENSSARG00000005798	13 retrocopies	retro_sara_172, retro_sara_208, retro_sara_228, retro_sara_273, retro_sara_319, retro_sara_334 , retro_sara_393, retro_sara_527, retro_sara_578, retro_sara_627, retro_sara_641, retro_sara_656, retro_sara_740,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Tarsius syrichta	ENSTSYG00000001483	17 retrocopies	retro_tsyr_1273, retro_tsyr_1274, retro_tsyr_1499, retro_tsyr_153, retro_tsyr_1705, retro_tsyr_1858, retro_tsyr_1869, retro_tsyr_2152, retro_tsyr_262, retro_tsyr_327, retro_tsyr_346, retro_tsyr_600, retro_tsyr_636, retro_tsyr_684, retro_tsyr_808, retro_tsyr_865, retro_tsyr_905,
Vicugna pacos	ENSVPAG00000000279	4 retrocopies	retro_vpac_214, retro_vpac_255, retro_vpac_26, retro_vpac_357,