RetrogeneDB ID: retro_dord_556

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_31787:4033..4741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ola1
• Ensembl ID: ENSDORG00000008681
• Aliases: None
• Description: Obg-like ATPase 1 [Source:MGI Symbol;Acc:MGI:1914309]

Sequence

>retro_dord_556
CCCCAAAAGGCAGGTGATGGAATTAAACCACCCCCAATCATTGGAAGATTTGGAACCTCACTGAAAATTGGCATTGCTGG
ATTACCAAATGTTGGGAAATCTACATACCTCAATGTATTAACTGATAGTCAGACCTCTGCAGAAAACTTCCCATTTTGTA
CTATTGATCCTAATGAGAGCAGAGTACCTGTGCCAGATGAAAGATTTGACTTTCTTTGTCAATATCACAAACCAGCAAGC
AAAATTCCCGCCTTTCTAAATGTAGTGGATATTGCTGGTCTTGTGAAAGGAGCTCACAACGGGCAGGGCCTGGGAAATGC
CTTTTTATCTCATATTAGTGCCTGTGATGGAATCTTCCATCTAACACATGCTTTTGAAGATGAATATATCACACACGTGG
AAGGAAGTGTAGATCCCATCTGTGACATAGAAAAAATACATGAAGAACTTCAGCTTAAAGATGAGGAAATGATTGTTCCC
ATTATAGATAAACTAGAAAAGGTGGCTGTCAGAGGCAGAGATAAAAAACTAAAACCTGAATATGACATAATGTGCAAGGT
CAAATCCTGGGTTATAGATCAAAAGAAACCTGTTTGTTTCTAACATGATTGGAATGACAAAGAGATTGAAGTGTTGAATA
AACACTTATTTTTGACTTCAAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGACTACGTTAGG

Alignment

ORF - retro_dord_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 59.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKKAGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDERFD
          P.KAGDGIKPPPIIGRFGTSLKIGI.GLPNVGKST..NVLT.SQ.SAENFPFCTIDPNESRVPVPDERFD
Retrocopy PQKAGDGIKPPPIIGRFGTSLKIGIAGLPNVGKSTYLNVLTDSQTSAENFPFCTIDPNESRVPVPDERFD

Parental  FLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVDPI
          FLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLT.AFED..ITHVEGSVDPI
Retrocopy FLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTHAFEDEYITHVEGSVDPI

Parental  RDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKEIE
          .DIE.IHEELQLKDEEMI.PIIDKLEKVAVRG.DKKLKPEYDIMCKVKSWVIDQKKPV.F.HDWNDKEIE
Retrocopy CDIEKIHEELQLKDEEMIVPIIDKLEKVAVRGRDKKLKPEYDIMCKVKSWVIDQKKPVCF*HDWNDKEIE

Parental  VLNKHLFLTSKPMVYLVNLSEKDYIR
          VLNKHLFLTSKPMVYLVNLSEKDY.R
Retrocopy VLNKHLFLTSKPMVYLVNLSEKDYVR

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_556 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556 ,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,