RetrogeneDB ID: retro_dord_686

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_55:312403..312708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Spcs1
• Ensembl ID: ENSDORG00000000678
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1916269]

Sequence

>retro_dord_686
ATGCAGGAATATCTCAGCGCACTCGCCACAGAGATGGCTTACAAGGGGCAGAAGCTAGCTGAACAGATGTTTCCAGGAAT
TATTCTTTTTTCTGCAATAGTTGGATTTATCTATGGGTGCGTGGCTGAACAGTTCGGGTGGACAGTCTATATAGTTATGG
CCAGATTTGCTTTTTCGTGTTTGCAGACACTTCCTCCATAGCCGTCTAACGAACACATCCCCTCAATTGGTTACCTGTTC
ATGACTTAGGAAGAGAAGACAAGAAAACAGGGGATAGAAAATTTAAGAGGCATGCTAAAAATAAT

Alignment

ORF - retro_dord_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLEHLSALPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWP-I
          M.E.LSAL.T.M.YKGQKLAEQMF.GIILFSAIVGFIYG.VAEQFGWTVYIVMA.FAFSCL.TLPP.P..
Retrocopy MQEYLSALATEMAYKGQKLAEQMFPGIILFSAIVGFIYGCVAEQFGWTVYIVMARFAFSCLQTLPP*P<V

Parental  YRRHPLKWLPVQDSGTEDKKTGDRKIKRHAKNN
          .R.HPL.WLPV.D.G.EDKKTGDRK.KRHAKNN
Retrocopy *RTHPLNWLPVHDLGREDKKTGDRKFKRHAKNN

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_686 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686 , retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,