RetrogeneDB ID: retro_opri_1152

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8083:27869..28409(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSOPRG00000004055
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_opri_1152
GAAGGGAACTTCTCTCCCAAGTCCAACGAAAAAGATGGGCCAGTGGAGAAAAAGAGCCAGAATGGCCCATACGAGGTTGA
AAATGTCAGGTCTCAGAACCCTGCAGGTCGGACAGGCCTGGCTGGCCAAGGGCTCCTGGGACGCTGGGGCCCCAGCCATG
TTGCTGACCCTTTTATAACCAGGTGGAAAAGGGGCAGCGAGGGGAATCAAGTTACCCATCCGGTTTCTGGCAACAACTCC
CTGCAATTTGTAGCCGTCCAAAGGAAGGACTGTGGAGAATGGGCCATTCCTGGTGGGATGGTGGATCCGGGTGCCACTCT
GCAGAGGGAATTTGGAGAGGAAGCCATGAATGCCTTACAGAAATCCAGGATGAAAAGGCGGAAATTGGAGAAACAACTGC
ACCTGCTCTTCAGCCAGGACAAGTTTGAGGTCTATAAGGGCTACGTGGATGATCCACGTAGCACAGATAATGCGTGGGTG
GAGACGCAGGTTGTGAACTACCCTGAGGACATGGGGAAAACGGCCCACCACCTTCTGCTG

Alignment

ORF - retro_opri_1152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 58.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETNFSPKFNEKDGHVERKSQNGLYEIQNGRPRNPVGRTGLVGRGLLGRWGPNHAADPIITRWKKDGSGSK
          E.NFSPK.NEKDG.VE.KSQNG.YE..N.R..NP.GRTGL.G.GLLGRWGP.H.ADP.ITRWK....G..
Retrocopy EGNFSPKSNEKDGPVEKKSQNGPYEVENVRSQNPAGRTGLAGQGLLGRWGPSHVADPFITRWKRGSEGNQ

Parental  VTHPVSRKRVLQFVAIKRKDCGEWAIPGGMVEPGEKISAALKREFGEEALNSLQKSSAEKKKIEQQLHRL
          VTHPVS....LQFVA..RKDCGEWAIPGGMV.PG....A.L.REFGEEA.N.LQKS.....K.E.QLH.L
Retrocopy VTHPVSGNNSLQFVAVQRKDCGEWAIPGGMVDPG----ATLQREFGEEAMNALQKSRMKRRKLEKQLHLL

Parental  FNQDHLVIYKGYVDDPRNTDNAWMETEAVNYHDETGEVMDNLTL
          F.QD....YKGYVDDPR.TDNAW.ET..VNY....G.....L.L
Retrocopy FSQDKFEVYKGYVDDPRSTDNAWVETQVVNYPEDMGKTAHHLLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1152 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152 ,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,