RetrogeneDB ID: retro_dord_346

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_132:2093..2644(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000007147
• Aliases: None
• Description: None

Sequence

>retro_dord_346
CCCGGTGGTGGCTTCGAAACCCTGGGGATGGGGTGGGAGATGCCACGAAGCCCCATATAGGTTTCTTTAAGCCACCTTCG
ACTGGTTCTGGACAACTTAGAAGTGTTCTGCCACCCAGAGACCGACCAGAGCCTGATCATGGAACTTCTGGAGCTGCAGG
CCCACGTGTGGGGCGAAGCGGCTGCGCGGTACCATTTTGAGGACATCAGCTGGGTACAGGGCTCTAGGATCCAGCAGGTG
GAGTCGGTGCACCCCTCACTTTGGAGAACCTGGCCCTGAGGGGCTGCTGCCAAGAAGCCTGACTCCTCTCTGGGAAACAG
CAGATAGCTACAGGGAGCCAGCAGGTAGCAAAGGATGTGACACTACATCAAGCTTTGCTTCTGCTGCCCCAGTACCAAAC
TGATCTCTTGCTCACCTTCAACCAACCCCTCTCTGAGAACAGGTCATCTCTTGGTCCTGAAAATCTGTCACCTCCACCCT
GGAGCCTGAGTAACTTTGAACAACTAGTGACCAGTCTGACCCTCCAGGATCCCAACATCTTTGGTCCCCAG

Alignment

ORF - retro_dord_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTRDFPLFGGAFSVILPPGAIDVSDLRPVPDNQEVFCHPETDQSLIVELLELQAHVQGEAAARYHFEDVG
          P...F...G........P.....S.LR.V.DN.EVFCHPETDQSLI.ELLELQAHV.GEAAARYHFED..
Retrocopy PGGGFETLGMGWEMPRSPI*VSLSHLRLVLDNLEVFCHPETDQSLIMELLELQAHVWGEAAARYHFEDIS

Parental  WVQEARIQQVESVQP-LTLENLALRGCCQEAWLLSGKQQITKGSQQVAKDVTLHQALLRLPQYQTDLLLT
          WVQ..RIQQVESV.P.LTLENLALRGCCQEA.LLSGKQQI..GSQQVAKDVTLHQALL.LPQYQTDLLLT
Retrocopy WVQGSRIQQVESVHP<LTLENLALRGCCQEA*LLSGKQQIATGSQQVAKDVTLHQALLLLPQYQTDLLLT

Parental  FNQPPSENRSSLGPENLSPPPWSLSNFEQLVTSLTLHDPNIFGPQ
          FNQP.SENRSSLGPENLSPPPWSLSNFEQLVTSLTL.DPNIFGPQ
Retrocopy FNQPLSENRSSLGPENLSPPPWSLSNFEQLVTSLTLQDPNIFGPQ

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_346 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012555	1 retrocopy	retro_chof_14,
Dasypus novemcinctus	ENSDNOG00000018164	1 retrocopy	retro_dnov_2261,
Dipodomys ordii	ENSDORG00000007147	2 retrocopies	retro_dord_325, retro_dord_346 ,
Macropus eugenii	ENSMEUG00000006399	2 retrocopies	retro_meug_1091, retro_meug_220,
Mus musculus	ENSMUSG00000032892	2 retrocopies	retro_mmus_175, retro_mmus_2983,
Rattus norvegicus	ENSRNOG00000004980	4 retrocopies	retro_rnor_1148, retro_rnor_2982, retro_rnor_2983, retro_rnor_759,