RetrogeneDB ID: retro_sara_438

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_207766:8874..9298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000005945
• Aliases: None
• Description: None

Sequence

>retro_sara_438
GAAATCCAGCGTTTGCTGGCAGAACCAGTTCCTAGCATTAAAGCAGAACCAGATGAGAGCAACACCTGTTATTTTCATGT
GGTCATTGCTGGCCCCCAGGATTCCCCCTTTGAGGGAGGGACTTTTAAACTTGAACTATTCCTTCCAGAAGAATACCCAA
TGACAGCCCCTAAAGTACGTTTTATGACCAAAATTTATCATCCTAATGTAGACAAGTTGAGAAGAACATGTTTAGATATT
TTGAAAGATAAGTGGTCCCCAGCTCTGCAGATCTGCACAGTTCTGCTATCGATCCAGCTTTGTTAAGTGCTCCCAATCCA
GATGATCATTAGCAAATGATGTAGCGGAGCAGTGGAAAACCAACGAAGCCCAAGCCATAGAAACAGCTAGAGCATGGACT
AGGCTATATGCCATGAATAATATT

Alignment

ORF - retro_sara_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNV
          E.QRLLAEPVP.IKAEPDESN..YFHVVIAGPQDSPFEGGTFKLELFLPEEYPM.APKVRFMTKIYHPNV
Retrocopy EIQRLLAEPVPSIKAEPDESNTCYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMTAPKVRFMTKIYHPNV

Parental  DKLGRICLDILKDKWSPALQIRTVLLSIQ-ALLSAPNPDD-PLANDVAEQWKTNEAQAIETARAWTRLYA
          DKL.R.CLDILKDKWSPALQI.TVLLSIQ.ALLSAPNPDD..LANDVAEQWKTNEAQAIETARAWTRLYA
Retrocopy DKLRRTCLDILKDKWSPALQICTVLLSIQ<ALLSAPNPDD<SLANDVAEQWKTNEAQAIETARAWTRLYA

Parental  MNNI
          MNNI
Retrocopy MNNI

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_438 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 19 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009833	1 retrocopy	retro_amel_507,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Felis catus	ENSFCAG00000004260	2 retrocopies	retro_fcat_1477, retro_fcat_1598,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Myotis lucifugus	ENSMLUG00000009982	2 retrocopies	retro_mluc_2166, retro_mluc_453,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Otolemur garnettii	ENSOGAG00000034461	7 retrocopies	retro_ogar_1502, retro_ogar_2178, retro_ogar_406, retro_ogar_408, retro_ogar_566, retro_ogar_584, retro_ogar_732,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sorex araneus	ENSSARG00000005945	3 retrocopies	retro_sara_174, retro_sara_438 , retro_sara_695,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,