RetrogeneDB ID: retro_dord_45

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1227:57150..57626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Csnk2b
• Ensembl ID: ENSDORG00000014179
• Aliases: None
• Description: casein kinase 2, beta polypeptide [Source:MGI Symbol;Acc:MGI:88548]

Sequence

>retro_dord_45
CCTGATGAAAAGCTGGAAGATAGCCCCCACCAGAGTGACCTGATGGAGCAGGCCGCCGAGATGCTTTAGGGATTGACCCA
CGCTCACTACATCCTCACCAACCGTGGCATCACCCAAACAATGGAAAAGTACCAGCAAGGGAGACTTTGGCTACTGGCCC
CGTGTGTACAGTGAAAATCAGCCAATGCTTCCCATCATCCTTTCAGATATCCTAGGCGAGGCTGTGGGTGAAGCTCTACT
GCCCCAAGTGCATGAATGTGTGCACACCCAAATCACGAAGCACCATCACGTAGAAGGCGACTACTTAGGCACCAGTTTCT
ATCACATGCTCTTCATGGTGCATCGAGAGTACCAGCCCTGGCGGCCTGCCAACTAGGCCTGTACCCAGGCTTTGTTGTTT
CAAGATCCAGCCAATGGCTTACCAGCTGCAACTCCAAACCGCCAGCAACTTCAAGAGGCCAGACAAGACCATTCGC

Alignment

ORF - retro_dord_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.31 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQG-DFGYCPRVYCENQPMLPIGLSD
          PDE.LED.P.QSDL.EQAAEML.GL.HA.YILTNRGI.Q..EKYQQG.DFGY.PRVY.ENQPMLPI.LSD
Retrocopy PDEKLEDSPHQSDLMEQAAEML*GLTHAHYILTNRGITQTMEKYQQG>DFGYWPRVYSENQPMLPIILSD

Parental  IPGEAM-VKLYCPKCMDVYTPKS-SRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPAN-QFVPRLYGFKIH
          I.GEA..VKLYCPKCM.V.TPKS...HHH..G.Y.GT.F.HMLFMVH.EY.P.RPAN...VPRL..FKI.
Retrocopy ILGEAV>VKLYCPKCMNVCTPKS<TKHHHVEGDYLGTSFYHMLFMVHREYQPWRPAN>RPVPRLCCFKIQ

Parental  PMAYQLQLQAASNFKSPVKTIR
          PMAYQLQLQ.ASNFK.P.KTIR
Retrocopy PMAYQLQLQTASNFKRPDKTIR

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_45 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 16 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005751	1 retrocopy	retro_acar_107,
Bos taurus	ENSBTAG00000008837	1 retrocopy	retro_btau_885,
Callithrix jacchus	ENSCJAG00000002996	1 retrocopy	retro_cjac_2700,
Dasypus novemcinctus	ENSDNOG00000018728	1 retrocopy	retro_dnov_697,
Dipodomys ordii	ENSDORG00000014179	1 retrocopy	retro_dord_45 ,
Erinaceus europaeus	ENSEEUG00000006417	2 retrocopies	retro_eeur_331, retro_eeur_555,
Echinops telfairi	ENSETEG00000015168	3 retrocopies	retro_etel_225, retro_etel_271, retro_etel_769,
Felis catus	ENSFCAG00000007642	2 retrocopies	retro_fcat_1749, retro_fcat_206,
Macropus eugenii	ENSMEUG00000004095	10 retrocopies	retro_meug_1158, retro_meug_1316, retro_meug_1598, retro_meug_187, retro_meug_1939, retro_meug_40, retro_meug_525, retro_meug_528, retro_meug_751, retro_meug_752,
Monodelphis domestica	ENSMODG00000015287	4 retrocopies	retro_mdom_1433, retro_mdom_1558, retro_mdom_704, retro_mdom_936,
Mustela putorius furo	ENSMPUG00000011129	1 retrocopy	retro_mputfur_154,
Oryctolagus cuniculus	ENSOCUG00000023483	2 retrocopies	retro_ocun_1477, retro_ocun_362,
Ochotona princeps	ENSOPRG00000012138	1 retrocopy	retro_opri_970,
Sarcophilus harrisii	ENSSHAG00000001478	2 retrocopies	retro_shar_672, retro_shar_693,
Sus scrofa	ENSSSCG00000001414	1 retrocopy	retro_sscr_538,
Tursiops truncatus	ENSTTRG00000014103	2 retrocopies	retro_ttru_1595, retro_ttru_1740,