RetrogeneDB ID: retro_dord_15

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_41069:1867..2527(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000008350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000016606
• Aliases: None
• Description: None

Sequence

>retro_dord_15
GTGACTTGTAAAAAGTGTGTGGTGGTGGGTAATGGAGGAGTTTTGAAGAATAAGAAGTTAAGAGAAACTATCGACTCGTA
TGATGTTGTCATAAGAATGAATAATGGTCCTGTTTTAGGACATGAAGAGGAAGTTGGGACACGCACAACCTTCCGACTTT
TTTATCCAGAATCTGTTTTTTCAGATAGCAGTCATAATGATCCTAACACAATAGCCATTTTTGTGGCTTTTAAGAAAAAT
GATTTGGACTGGATGCTGAAATTGCTGGCCAATGGTCGTATATTCCTCAAGAATTTTTGGAAGAAACCAGCCTTAAAGTT
GATCTATAAACCACATCAAATCAGAATATTAGATCCTTTCCTTATCAGGACAACAGCTTATGAACTGCTTCATTTTCGAA
AAAATCTTCCCAGATTTAAGAAACAAAAACACCCAACAATGGGAATAATTGCCATTGTATTGGCATTTCACATCTGTCAT
GAAGTTCACATAGCTGGTTTTAAATACAACTTTTCTGACCTCATGAGCCCTTTGCACTACTATGGGAATGCCACTATGTC
TTCAATGAAGAAGAACACAAATCACAATGTGGCTGCAGAACAAGTCTTTTTGAACTACATTACAAAAAATAACTTTGTCA
TTAACTTGACTGAAGATTGA

Alignment

ORF - retro_dord_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.63 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPCKKCVVVGNGGVLKNKTLGEKIDSYDVIIRMNNGPVLGHEEEVGRRTTFRLFYPESVFSDLNHNDPNT
          V.CKKCVVVGNGGVLKNK.L.E.IDSYDV.IRMNNGPVLGHEEEVG.RTTFRLFYPESVFSD..HNDPNT
Retrocopy VTCKKCVVVGNGGVLKNKKLRETIDSYDVVIRMNNGPVLGHEEEVGTRTTFRLFYPESVFSDSSHNDPNT

Parental  TAILVAFKPLDLKWLMELLAGGKINTNGFWKKPALNLIYKPYQIRILDPFIIRTAAYELLHFPKTFPKNQ
          .AI.VAFK..DL.W...LLA.G.I....FWKKPAL.LIYKP.QIRILDPF.IRT.AYELLHF.K..P...
Retrocopy IAIFVAFKKNDLDWMLKLLANGRIFLKNFWKKPALKLIYKPHQIRILDPFLIRTTAYELLHFRKNLPRFK

Parental  KPKHPTTGIIAITLAFHICHEVHLAGFKYNFSDLKSPLHYYGNATMSLMNKNAYHNVTAEQLFLKDIIEK
          K.KHPT.GIIAI.LAFHICHEVH.AGFKYNFSDL.SPLHYYGNATMS.M.KN..HNV.AEQ.FL..I...
Retrocopy KQKHPTMGIIAIVLAFHICHEVHIAGFKYNFSDLMSPLHYYGNATMSSMKKNTNHNVAAEQVFLNYITKN

Parental  NFVINLTQD
          NFVINLT.D
Retrocopy NFVINLTED

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_15 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013240	2 retrocopies	retro_cpor_1321, retro_cpor_1338,
Dipodomys ordii	ENSDORG00000016606	1 retrocopy	retro_dord_15 ,