RetrogeneDB ID: retro_sara_539

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_231918:449..1307(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSSARG00000011475
• Aliases: None
• Description: chaperonin containing TCP1, subunit 7 (eta) [Source:HGNC Symbol;Acc:1622]

Sequence

>retro_sara_539
GAAATGGCCCTTTTAAATGTTGAATTTGAAAGGAAAGTTGAAAAGGATAATGCTGAAATGAGGGTCCATACAGTTGAGGA
TTATCAGGCAATTGTTAATGCTGAGAAGGATATTCACTGTGAAAATTTAGAAAGGATTCATCTTCTGGAGCCAGTCATCT
TATCCGAACACCTTGTTGGGGGTGTGGCTACACAGTACTTTGCCGACAGGGACTATTCAGTGCTGGCCAAGTGTGAGAGG
AAGATCTGAAGGACAATAATAGTTGTGGAGGCTCTATACAAACTAGTATGGACACTCTAGAATGAGAGGTACTGGGTGGC
TGCCAGGGCTTTCAGGAGACCCAGATTGGATATGAGATATACAGTTTCTTCACTGGCTGTCCCAAGGCCAAGACTAGCAC
TGTCATCCTCTGAGGTGGTGCTGAACAGTTTGTAGAGGATACTGAGTTGTCTCTGTATGATGTCATCATGATGATCAGGA
GAGCCATCAAGAACAATTTGATGGTGGCTGTTAGTGGAGCTATTGAGATGGAGCTCTCCAAGGAGCTGCAGAAATACTCA
AGGACCATTCCAGAGAAGCAGCAGCTACTTATTGGAACATATGAAAGGCCTTGAAAATCATTTTGAGCTAGCTATGTGAC
AATGCTGGTTTTGATGCTACCAACATCCTCAATAAGCTGCAGGGTCTGCATGCCCAGGGAGCCATGTGGTGGTATGGAAT
GAATATCAACAATAATGATATTGCTGACAACTTTGCAGTCTTCTTGTGGGAGCCAGCTGTGGTGTGGTAAATGCCATGGC
TGCAGCTCCAGAGTCTGCATGCCTCACTGTGTCCATAGATGAAACCATCAAGAACCCT

Alignment

ORF - retro_sara_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.18 %
• Parental protein coverage: 53.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KIALLNVELELKAEKDNAEVRVHTVEDYQAIVDAEWDILYEKLERIHRSGAKVILSKLPIGDVATQYFAD
          ..ALLNVE.E.K.EKDNAE.RVHTVEDYQAIV.AE.DI..E.LERIH.....VILS....G.VATQYFAD
Retrocopy EMALLNVEFERKVEKDNAEMRVHTVEDYQAIVNAEKDIHCENLERIHLL-EPVILSEHLVGGVATQYFAD

Parental  RD-MFCAGRVPEEDLKRTMMACGGSIQTSVNALGPEVLGSCQVFEETQIGCERYNFFTGCPKAKTCTIIL
          RD..F.AG.V.EEDLK.....CGGSIQTS...L..EVLG.CQ.F.ETQIG.E.Y.FFTGCPKAKT.T.IL
Retrocopy RD<LFSAGQV*EEDLKDNN-SCGGSIQTSMDTLE*EVLGGCQGFQETQIGYEIYSFFTGCPKAKTSTVIL

Parental  RGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLRDYSRTIPGKQQLLIGAYA-KALE
          .GGAEQF.E.TE.SL.D.IM..RRAIKN...VA..GAIEMELSK.L..YSRTIP.KQQLLIG.Y..KAL.
Retrocopy *GGAEQFVEDTELSLYDVIMMIRRAIKNNLMVAVSGAIEMELSKELQKYSRTIPEKQQLLIGTYE<KALK

Parental  IIPRQLCDNAGFDATNILNKLRARHAQGGM-WYGVDVNNEDIADNFEAFVWEPAMV-RINALTAASEAAC
          II...LCDNAGFDATNILNKL...HAQG.M.WYG...NN.DIADNF..F.WEPA.V...NA..AA.E.AC
Retrocopy IILS*LCDNAGFDATNILNKLQGLHAQGAMWWYGMNINNNDIADNFAVFLWEPAVV<VVNAMAAAPESAC

Parental  LIVSVDETIKNP
          L.VS.DETIKNP
Retrocopy LTVSIDETIKNP

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_539 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Sorex araneus	ENSSARG00000011475	1 retrocopy	retro_sara_539 ,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,