RetrogeneDB ID: retro_dord_315

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1134:137469..138165(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Parl
• Ensembl ID: ENSDORG00000014935
• Aliases: None
• Description: presenilin associated, rhomboid-like [Source:MGI Symbol;Acc:MGI:1277152]

Sequence

>retro_dord_315
GGGTCATGTAGGGAAGCTTACAAGAGAAGCGCTTTGATTTCTCCTATAGAAGACGTCATTTCTTATCCAGGAATATCCCC
ATCAGGACCCTCATGAAACTTTTCTTCATTGTGGGGTTAACAGGCTGTGCATCATTTGGTTCAGCTGCTGTTTGATCATG
TAAGTCACTGAAATCCAGAGTCTGGAGTTCTTTTGATGGCCTAAAAGTTGATTGGTTGGATGGCAGAAGGCCACACAAAG
AAGGAAACCTCAGAAAAGAGATTCGCAAGTGGTAGAATAACCTAAGTGGTGGCCAGTAACTGTGTGTAAGCAATCATAGC
TGCAGATGTCTTTGTATTCTATTTATGGAGAGTATTTTACCATAGACAATGATCAGATAACTCGCATTAAATACAGCCGC
AGAGGGCCTTTGCTCTCTCAGGGTGATGTCGACATCTCATCCTTTCTCCTTATTTCACATGGAAGCAAATATGCACATTT
TGTGGAGCTTTCCTTCCAGCCTCATGAACATTCCGGTCAGGAGCTGTTCATGGCAGTGGACCTGTCTGCAGGTATTATTT
CCAATTGTGTCAGTTATGTGTGTAAAGTTGCCAGAGGAAGATATAGCCTTTCACATGGTGCATCAGGTGTGACTGTGCTC
TACTTTCAATGGTCAGCACTCAGATCCTCGATGGGAGGCTCGCCATCATCTTCCTC

Alignment

ORF - retro_dord_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.4 %
• Parental protein coverage: 61.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSSGEAYKRSALIPPVEETIFYPS-PYPIRTLVKPFFFTVGFTGCA-FGSAAIWQYESLKSRVQSYFDGL
          GS..EAYKRSALI.P.E..I.YP....PIRTL.K..FF.VG.TGCA.FGSAA.....SLKSRV.S.FDGL
Retrocopy GSCREAYKRSALISPIEDVISYPG<NIPIRTLMK-LFFIVGLTGCASFGSAAV*SCKSLKSRVWSSFDGL

Parental  KADWLDSIRPQKEGDLRKEINKWWNNLSDGQRTVTGIIAANVCVFCLWRVPSLQRTMIRYFTSNPASKVL
          K.DWLD..RP.KEG.LRKEI.K.W.N...G............C...L.....L..TMIR....N.A...L
Retrocopy KVDWLDGRRPHKEGNLRKEIRK-W*NNLSGGQ*LCVSNHSCRCLCILFMESILP*TMIR*LALNTAAEGL

Parental  CSPMLLSTFSHFSLFHMAANMYVLWSFSSSIVNI-LGQEQFMAVYLSAGVISNFVSYVCKVATGRYGPSL
          CS....ST...FSLFHM.ANM..LWSF.SS..NI..GQE.FMAV.LSAG.ISN.VSYVCKVA.GRY..S.
Retrocopy CSLRVMSTSHPFSLFHMEANMHILWSFPSSLMNI<SGQELFMAVDLSAGIISNCVSYVCKVARGRYSLSH

Parental  GASGAIM-TVLAAVCTKIPDGRLAIIFL
          GASG......L..V.T.I.DGRLAIIFL
Retrocopy GASGVTV<ALLSMVSTQILDGRLAIIFL

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_315 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315 ,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Myotis lucifugus	ENSMLUG00000004507	1 retrocopy	retro_mluc_883,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Oryctolagus cuniculus	ENSOCUG00000007882	1 retrocopy	retro_ocun_541,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pongo abelii	ENSPPYG00000014338	2 retrocopies	retro_pabe_2290, retro_pabe_2912,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,