RetrogeneDB ID: retro_sara_592

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_236317:288333..288935(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSSARG00000012111
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:HGNC Symbol;Acc:21906]

Sequence

>retro_sara_592
GAGAACATCACTGTGGTGAAGGGCATCTGGCTTCTGGAAAATGTCATCCATCTTACGAAGGAAACCTCCCTTGGTTAGAA
GGCTCCTCACTATTTCCGTCCGTCTGGTGCCTCAGTTTCTGATAGAGTTGAAAAGAAGGAAATCTGAGGAACTGGCATGG
AGAAAACCAAGAGAGAACTTGCAATCCAGAAATGAATAAAGCAAAGCAAAGTATGGATCAGCTAACCAGAGCTACTCTTT
GAGAGAGAATATCAAGGGAGGAGGAACGCTAGAGGGCAAAAACCCTGGCTAAGCAGCTGCAAGAGAAGGATCAAATGGCT
TAAGAAGCAGGATGCATTCTCCAAAGAGCAGCTGGCTAGACTGGAGGAAAGGAATGCAGAGTTCTACAAGGTCACCACTG
AGCAGTATCAGAAGGCTGCCGAAGTGGTGGAGGGAAAGTTCAAGCAGTTTGAGTCTCATCCCTTTATACTGATCTGCAGG
CCCAGATTCTCCAGTGTTACTTCCAGAACTCCCAGCAGACCCCCAACTGCTCTGCTCTGCCCAGTCAGTACATGTTCTGT
GTCAATCATGCCAAACAGCATGGCCTAATTGAAAAGAGAGGA

Alignment

ORF - retro_sara_592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 92.24 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENITVVKGIRLSENVIDRMKETSPGSKSSRYSGPFGASVSDEELKRRVAEELALEKAKRESENQKRLKQS
          ENITVVKGI.L.ENVI...KETS.G.K...Y..P.GASVSD...K.........EK.KRE...QK..KQS
Retrocopy ENITVVKGIWLLENVIHLTKETSLG*KAPHYFRPSGASVSDRVEKKEI-*GTGMEKTKRELAIQK*IKQS

Parental  K-ELEQLTRAILRERISSEEERSKAKTLAKQLEERDRM-IKKQDAFYKEQLARLEERNSEFYKVTTEQYQ
          K....QLTRA.L.ERIS.EEER..AKTLAKQL.E.D.M..KKQDAF.KEQLARLEERN.EFYKVTTEQYQ
Retrocopy K<SMDQLTRATL*ERISREEER*RAKTLAKQLQEKDQM>LKKQDAFSKEQLARLEERNAEFYKVTTEQYQ

Parental  KAAEEVEGKFKRFETHP-ICTDLQAQILQCYRQNSKQTLNCSALASQYMRCVNHAKQQGMIEKGG
          KAAE.VEGKFK.FE.HP...TDLQAQILQCY.QNS.QT.NCSAL.SQYM.CVNHAKQ.G.IEK.G
Retrocopy KAAEVVEGKFKQFESHP<LYTDLQAQILQCYFQNSQQTPNCSALPSQYMFCVNHAKQHGLIEKRG

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_592 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592 ,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,