RetrogeneDB ID: retro_dord_373

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_14619:25381..25789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Apool
• Ensembl ID: ENSDORG00000011045
• Aliases: None
• Description: apolipoprotein O-like [Source:MGI Symbol;Acc:MGI:1915367]

Sequence

>retro_dord_373
TCTAGGTTTAAGAAAATTACCTATCCACTAGGACTGGCTACATTAGGAGCAACTGGTTGCTACCCAGCTCAGTCATTAAT
CATTGCAAAGATTACTGGGAAAAAAGCATATGTGACCAGCCAGCACATTTATGAAGCTGTTAAATCACTGTGGACAACAA
GCAACAAAAACAAATCACTCTCTAAACCTAAAGAAAAGACTGAGCTAGAAAGCCCCAATGAAACAGAAATGCCTGCAAAA
ACAACTCAAGTCCTGCAACATTCAGTGCCTTTACCAAAAGAACTCCACTCTGAAACAAAGACCAACTCAGCATTAACCTC
AGATTCTAAACAGTTGATATCTGACCCAAAGCTTATGGATCATGGGCAGTCCCATCCAGAAGATGTAGATATGTACAGCA
CTAGAAGC

Alignment

ORF - retro_dord_373 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.88 %
• Parental protein coverage: 72.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRFKKIAYPLGLATLGATVCYPAQSVIIAKVSGRKHMRPASTFMELLNRCGQQATKMNHSLNLKKKLRQL
          SRFKKI.YPLGLATLGAT.CYPAQS.IIAK..G.K.........E..........K.N.SL...K....L
Retrocopy SRFKKITYPLGLATLGATGCYPAQSLIIAKITGKKAYVTSQHIYEAVKSLWTTSNK-NKSLSKPKEKTEL

Parental  GSPNETEMPAKTTQVLNHSVPLPKELYSKIKTKSAFTSGTKQFISDPKLMDHGQSHPEDVDMYSTRS
          .SPNETEMPAKTTQVL.HSVPLPKEL.S..KT.SA.TS..KQ.ISDPKLMDHGQSHPEDVDMYSTRS
Retrocopy ESPNETEMPAKTTQVLQHSVPLPKELHSETKTNSALTSDSKQLISDPKLMDHGQSHPEDVDMYSTRS

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_373 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373 ,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tupaia belangeri	ENSTBEG00000010147	5 retrocopies	retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,