RetrogeneDB ID: retro_dord_468

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_20823:5497..5794(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Smim14
• Ensembl ID: ENSDORG00000001693
• Aliases: None
• Description: small integral membrane protein 14 [Source:MGI Symbol;Acc:MGI:1915802]

Sequence

>retro_dord_468
ATGGCAGAAGGTGGATTCGATCCCTGTGAATGTGTTTGCTCTCATGAACATGCAATGAGAAGGCTGATCAATCTGTTGCG
GCAATCCCAGTCCTACTGCACAGACACAGAATGTCTTCAGGAATTACCAGGACCTTCTGGTGACAATGGCAACAGTGTTA
CTATGATCCTGATGGCCTAGATGATTATTGCAGTGATCTTGTTCTTACTGAGACCACCTAATCTAAGAGGATCCAACCTA
CCTGGCAAGCCAACTAGTCCACATAATGGACAAGATCCACCAGCTCCTCCTGTGGAC

Alignment

ORF - retro_dord_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEGGFDPCECVCSHEHAMRRLINLLRQSQSYCTDTECLQELPGPSGDNGISVTMILMAWMVIAVILFLL
          MAEGGFDPCECVCSHEHAMRRLINLLRQSQSYCTDTECLQELPGPSGDNG.SVTMILMA.M.IAVILFLL
Retrocopy MAEGGFDPCECVCSHEHAMRRLINLLRQSQSYCTDTECLQELPGPSGDNGNSVTMILMA*MIIAVILFLL

Parental  RPPNLRGSNLPGKPTSPHNGQDPPAPPVD
          RPPNLRGSNLPGKPTSPHNGQDPPAPPVD
Retrocopy RPPNLRGSNLPGKPTSPHNGQDPPAPPVD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_468 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023287	1 retrocopy	retro_cfam_2156,
Dipodomys ordii	ENSDORG00000001693	2 retrocopies	retro_dord_468 , retro_dord_570,
Homo sapiens	ENSG00000163683	1 retrocopy	retro_hsap_3836,
Loxodonta africana	ENSLAFG00000002601	2 retrocopies	retro_lafr_1038, retro_lafr_158,
Mustela putorius furo	ENSMPUG00000006076	1 retrocopy	retro_mputfur_641,
Nomascus leucogenys	ENSNLEG00000017113	1 retrocopy	retro_nleu_2132,
Otolemur garnettii	ENSOGAG00000007152	4 retrocopies	retro_ogar_1971, retro_ogar_3123, retro_ogar_3370, retro_ogar_740,