RetrogeneDB ID: retro_dord_617

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_41156:2785..3707(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cct6a
• Ensembl ID: ENSDORG00000001249
• Aliases: None
• Description: chaperonin containing Tcp1, subunit 6a (zeta) [Source:MGI Symbol;Acc:MGI:107943]

Sequence

>retro_dord_617
GCAGCTAACATGGGCATGGATGTGCTAAGAACCAACCCAGGGCCCAAGGGCACAGTGAAGATGCTCATTTCTGGCACCGG
AGACATCACGCTGACTAAAGACAGCAATATGCTGCTGCACAAGATGCAAATTCAGAATCCAGCAGCCTCCGTAATAGCAA
GAGTAGCTCACAATGGCGCAACTGGTGATGGTACAACTTCCAACGTCCTTATCATTGGAGAGCTGCTGAAGCAGGCAGAT
CTCTACATTTCTGAGGAGCTTCATCTCAGAATCATCACTGAAGGTTTTGAAGCTGCAAAGGAAAAAGCCCTTCCATTACT
AGAACAAATCAAAGTAAACAGAGAGACAGATAGGGAAACACTTACAGAAGGGGACAGAAAATCTTTCCCTACTAATGTTC
ATGCTGAACGAGCAGATGTCTTAGCAGAGGCTGTAGTGGGCGCTATTTTGGCCATTAACAAAAGAGACGAGTCTATTGAC
TTGTTCATGGTTGAGATCATGAAAATGAAACATAAATCTGAAACGGACACAAGCTTAATAAAAGGACTTGTTTTGGATCA
TGGGGCACAGCATCCTGACATGAAGAGTAGAGCAGAAAATGTATACATCCTCACATGCGATGTGTCATTAGATATGAAAG
AACAGAAATGAATCCTGGATTTTTCTACGAGAGTGCAGAAGATAGAGGAAAAACTAGTAAAAGATGAAAGAAAATGTACT
GAAGATAAAGTTTAAAAAATTAATAGAACTGAAAAGGAAAGTTTGTGGAGATACAGATAAAGGGTTTATTGTTATTAACC
GGAAGGCAATTAACCTGTTTTCCTTAGATGCTCGTGCAAAAGAAGGCATAGTAGCTCTGTGCAGAGCTAAAAGAAGAAAT
ACAGAGAGACTGACTCTCGCTTGTGGTGGGGTAACTCTAAAT

Alignment

ORF - retro_dord_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 58.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSN
          AA....DVLRTN.GPKGT.KML.SG.GDI.LTKD.N.LLH.MQIQ.P.AS.IA.VA......TGDGTTSN
Retrocopy AANMGMDVLRTNPGPKGTVKMLISGTGDITLTKDSNMLLHKMQIQNPAASVIARVA--HNGATGDGTTSN

Parental  VLIIGELLKQADLYISEGLHPRIITEGFEAAKDKALQFLEQIKVNKEMDRETLIDVARTSLRTKVHAELA
          VLIIGELLKQADLYISE.LH.RIITEGFEAAK.KAL..LEQIKVN.E.DRETL....R.S..T.VHAE.A
Retrocopy VLIIGELLKQADLYISEELHLRIITEGFEAAKEKALPLLEQIKVNRETDRETLTEGDRKSFPTNVHAERA

Parental  DVLTEAVVDSILAIKKKDEPIDLFMVEIMEMKHKSETDTSLIRGLVLDHGARHPDMKKRVENAYILTCNV
          DVL.EAVV..ILAI.K.DE.IDLFMVEIM.MKHKSETDTSLI.GLVLDHGA.HPDMK.R.EN.YILTC.V
Retrocopy DVLAEAVVGAILAINKRDESIDLFMVEIMKMKHKSETDTSLIKGLVLDHGAQHPDMKSRAENVYILTCDV

Parental  SLE-YEKTEVSSGFFYKSAEER-EKLVKAERKFIEDKV-KKVIELKRKVCGDSDKGFIVINQKGIDPFSL
          SL..YE.TE...GFFY.SAE.R.EKLVK.ERK..EDKV.KK.IELKRKVCGD.DKGFIVIN.K.I..FSL
Retrocopy SLD<YERTEMNPGFFYESAEDR>EKLVKDERKCTEDKV>KKLIELKRKVCGDTDKGFIVINRKAINLFSL

Parental  DAFAKEGIVALRRAKRRNMERLILACGGVALN
          DA.AKEGIVAL.RAKRRN.ERL.LACGGV.LN
Retrocopy DARAKEGIVALCRAKRRNTERLTLACGGVTLN

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_617 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 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617 ,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,