RetrogeneDB ID: retro_dord_208

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5597:28474..28858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000008339
• Aliases: None
• Description: None

Sequence

>retro_dord_208
CGACAACAGAAGAAAAGGCAAGAAGAAATTAAAAGATGAGAAGAATCTGAAGAACCTCAAGTGCTAACACCAGAAGAATA
ATTAGCAGATAAACTGTGGCTACAGAAACTACAGGAAGATTCAGACCTTGTACTAGCAAAAGAAACTTTTGGTGTGAATG
ATACAGTTTGTGGGATAGATGCTATGAACCCATCTTCAAGAGATGATCTCACAGAATTCGGGAAGTTACTAAAAGATAAA
ATTATACAGGATGAAAAGTCATTCTATTATGCCAGGTTTTTGAAAGCCTTAGTTCGAGATGTGTGAATTTCGTTGGAAAT
TGATGACTTGCCAAAGATGACCAAATCATTGACTGTGCTTTGTTGTGAGAACACAGAAGCAAGA

Alignment

ORF - retro_dord_208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 59.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQQKKRQEEIKKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVCGIDAMNPSSRDD
          RQQKKRQEEIK.R.EE.EEP.VLTPEE.LADKL.L.KLQE.SDL.LAKETFGVN.TVCGIDAMNPSSRDD
Retrocopy RQQKKRQEEIK-R*EESEEPQVLTPEE*LADKLWLQKLQEDSDLVLAKETFGVNDTVCGIDAMNPSSRDD

Parental  FTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDL-KRTNSLTVLCSEKQKEK
          .TEFGKLLKDKI.Q.EKS.YYA.FL.ALVRDV.ISLEIDDL.K.T.SLTVLC.E.....
Retrocopy LTEFGKLLKDKIIQDEKSFYYARFLKALVRDV*ISLEIDDLPKMTKSLTVLCCENTEAR

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_208 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208 , retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,