RetrogeneDB ID: retro_sara_458

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_215238:5829..6098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSSARG00000010860
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_sara_458
ATGGCAGCCCCAGCGCTGGCAGGGCAGGTGCGACTCAGCGCGTGCAGCCTGAGGGCCTTGCAAGCCCAAGACTCAAATTC
TATCAGTCTGGTAAATGCGACGCCCATAGTGGCTCCATTCAAGAGGGTGGTGGAACCTTCGCCAGAAGAGAGAAGGCAGA
GGAGGAGCACTACTTCCCAGCACGATCTAAGGAACAGCTGGAAGCCTTGAAACAGCATCATGAAGATGAGATCACTATAC
ATAAGAAGGACATTGAGCATCTGCAGAAA

Alignment

ORF - retro_sara_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 82.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPALAAQVRLGVCGLRALQARG-IKSDQSGKFDSQSGSIREGGGAFARREKAEEERYFRQRSKEQLEA
          MAAPALA.QVRL..C.LRALQA....K..QSGK.D..SGSI.EGGG.FARREKAEEE.YF..RSKEQLEA
Retrocopy MAAPALAGQVRLSACSLRALQAQD<LKFYQSGKCDAHSGSIQEGGGTFARREKAEEEHYFPARSKEQLEA

Parental  LRQHHEDEIDIHKKEIERLQK
          L.QHHEDEI.IHKK.IE.LQK
Retrocopy LKQHHEDEITIHKKDIEHLQK

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_458 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458 ,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,