RetrogeneDB ID: retro_dord_325

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1166:12313..12871(+)
• 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_325
ATGGAACCCAGAAGAGACATCCCATTGTTTGGGGGCGCCTTCTCAGTCATCCTTCCTCCAGGGGCTATTGATGTAAGCGA
CCTTCGACTGGTTCCGGACAACCAAGAAGTGCTCTGCCACCCAGAGACCAACCAGAGCCTGATCGTGGAACTTCTGGAGC
TGCAGGCCCACGTGCGGGGCAAAGCGGCTGCGCGGTACCATTTTGAGGACATCAGCTGGGTGCAGGGCACTAGGATCCAG
CGGGTGATGTGGGTGCAACCCCTCACTTTGGAGAACCTGACTCTGCGGGGCTGCTGCCAAGAAGCCTGGCTCCTCTCTGG
GAAACAGCAAATAACTAAAGGGAGCTAGCAGGTAGCAAAGGATGTGACACTACATCAGGCTTTGCTTCAGCTGCCCCAGT
ACCAAACTGATCTCTTGCTCACCTTCAACCAACCCCCCTCTGAGAACAGATCATCTCTTAGTCCTGAAAATCTGTCACCT
CCACCCTGGAGCCTGAGTAACTTTGAACAACTAGTGACCAGTCTGACCCTCCATGACCCCAACATCTTTGGTCCCCAG

Alignment

ORF - retro_dord_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPTRDFPLFGGAFSVILPPGAIDVSDLRPVPDNQEVFCHPETDQSLIVELLELQAHVQGEAAARYHFED
          MEP.RD.PLFGGAFSVILPPGAIDVSDLR.VPDNQEV.CHPET.QSLIVELLELQAHV.G.AAARYHFED
Retrocopy MEPRRDIPLFGGAFSVILPPGAIDVSDLRLVPDNQEVLCHPETNQSLIVELLELQAHVRGKAAARYHFED

Parental  VGWVQEARIQQVESVQPLTLENLALRGCCQEAWLLSGKQQITKGSQQVAKDVTLHQALLRLPQYQTDLLL
          ..WVQ..RIQ.V..VQPLTLENL.LRGCCQEAWLLSGKQQITKGS.QVAKDVTLHQALL.LPQYQTDLLL
Retrocopy ISWVQGTRIQRVMWVQPLTLENLTLRGCCQEAWLLSGKQQITKGS*QVAKDVTLHQALLQLPQYQTDLLL

Parental  TFNQPPSENRSSLGPENLSPPPWSLSNFEQLVTSLTLHDPNIFGPQ
          TFNQPPSENRSSL.PENLSPPPWSLSNFEQLVTSLTLHDPNIFGPQ
Retrocopy TFNQPPSENRSSLSPENLSPPPWSLSNFEQLVTSLTLHDPNIFGPQ

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_325 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,