RetrogeneDB ID: retro_dord_96

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2952:68698..69187(+)
• Located in intron of: ENSDORG00000006575

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pacrgl
• Ensembl ID: ENSDORG00000015625
• Aliases: None
• Description: PARK2 co-regulated-like [Source:MGI Symbol;Acc:MGI:1914018]

Sequence

>retro_dord_96
ATTTATTCTAAGGGAGATATTCCTTGCAGGTTGGTCCATGGTTCAAAAAAGCACAGATTATAATGGGAATGCTCTCCTGA
AATCCTTCCATTTGACCAGTTTCTTATTAGTTTAGCTGGGGGTCTGAGAGAAACAAAACATTCCTATACCTTTGTGGCCA
AGGAGAGTTTTAAAGAGTTATATTTATTTAAAGATGCTCCTGAAAAGGCTATACCTTTGCTACCTAGGCTGATTCTGGTG
CTAAAGGCAGCTCTGGTCTATTCAGATGATGAAGTGTTTGGGAGAGGGTTGCGTGACCTGGTATAGCTAAGTGTCATCCT
TGGTCCTTCTTCTAATGACCATCTGAAACACCTGCTGACAAGCCTTTCCAAGAGACTAATGAATAAGTTCAAGAAGCCCA
TCACTAGCACACTGCAGAAGCTTGAGCAGCACGGTGGAAATGCAAGCCTTACCATCATCAAATCCAAAATGGCAACCCAC
TGCTCTATC

Alignment

ORF - retro_dord_96 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.44 %
• Parental protein coverage: 65.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IYSKGGIPCRLVHGSIKHRLQWDCSPESLPFDPLLITLEG-LRETKHPYTFVSKEGFRELLLVKGASEKA
          IYSKG.IPCRLVHGS.KHRL.W.CSPE.LPFD..LI.L.G.LRETKH.YTFV.KE.F.EL.L.K.A.EKA
Retrocopy IYSKGDIPCRLVHGSKKHRL*WECSPEILPFDQFLISLAGGLRETKHSYTFVAKESFKELYLFKDAPEKA

Parental  VPLLPRLIPVLKAALIHSDDEVFVRGLSALVQLSVVVGPSLNDHLKHLLTSLSKRLMDKKFKEPITSALQ
          .PLLPRLI.VLKAAL..SDDEVF.RGL..LV.LSV..GPS.NDHLKHLLTSLSKRLM..KFK.PITS.LQ
Retrocopy IPLLPRLILVLKAALVYSDDEVFGRGLRDLV*LSVILGPSSNDHLKHLLTSLSKRLMN-KFKKPITSTLQ

Parental  KLEQHGGNASLLIIKSKIPTYCSI
          KLEQHGGNASL.IIKSK..T.CSI
Retrocopy KLEQHGGNASLTIIKSKMATHCSI

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_96 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96 ,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541, retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866,