RetrogeneDB ID: retro_dord_21

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_24677:1886..2357(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000009738
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000006369
• Aliases: None
• Description: None

Sequence

>retro_dord_21
GATTTTCTATTACAGCAGACCATGCTACGAATTAAGGATCCTAAGAAGTCACTGGATTTTTATACTAGAGTTCTTGGAAT
GACCCTACTCCAAAAACTTGATTTTCCTTTTATGAAATTTTCACTCTATTTCTTGGCTTATGAGGATAAAAATGACATCC
CCAAAGAGAAAAATGAAAGAATCGCATGGACATTCTCCAGAAAAGCCACACTTGAGTTGACACACAATTGGGGCACGGAA
GATGATGAGACCCAAAGTTACCACAATGGCAATTCAGACCCTTGGGGATTTGGTCACATTGGAATTGCTGTTCCTGATGT
TCATGGTGCTTGTAAAAGATTTGAAGAACTAGGAGTCAAATTTGTGAAGAAACCTGATGATGGTAAAATGAAAGGTCTGG
CATTTATTCAAGATCCTGATGGCTACTGGATTGAAATTTTGAATCCTAACAGTATAGCAACTATTGTGTAG

Alignment

ORF - retro_dord_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.72 %
• Parental protein coverage: 84.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFLLQQTMLRIKDPKKSLDFYTRVLGMTLLQKLDFPSMKFSLYFLAYEDKNDIPKEKNERIAWTFSRKAT
          DFLLQQTMLRIKDPKKSLDFYTRVLGMTLLQKLDFP.MKFSLYFLAYEDKNDIPKEKNERIAWTFSRKAT
Retrocopy DFLLQQTMLRIKDPKKSLDFYTRVLGMTLLQKLDFPFMKFSLYFLAYEDKNDIPKEKNERIAWTFSRKAT

Parental  LELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVHGACKRFEELGVKFVKKPDDGKMKGLAFIQDPD
          LELTHNWGTEDDETQSYHNGNSDP.GFGHIGIAVPDVHGACKRFEELGVKFVKKPDDGKMKGLAFIQDPD
Retrocopy LELTHNWGTEDDETQSYHNGNSDPWGFGHIGIAVPDVHGACKRFEELGVKFVKKPDDGKMKGLAFIQDPD

Parental  GYWIEILNPNSIATIV
          GYWIEILNPNSIATIV
Retrocopy GYWIEILNPNSIATIV

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_21 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21 ,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,