RetrogeneDB ID: retro_opri_405

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10973:42091..42493(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5A
• Ensembl ID: ENSOPRG00000011584
• Aliases: None
• Description: cytochrome b5 type A (microsomal) [Source:HGNC Symbol;Acc:2570]

Sequence

>retro_opri_405
ATGGCCGAGCAGTGCAACCAAGCTGTGAAGTACTACACCCTGGAAGAGATTAAGAAGCACAACCACAGCAAAAGCCCCTG
GCTGATCACCACACAAGGTGATCATTCACCTGACCAAATTCCTGGAGGAGCATCCTGCTGGGGAGGAAGTCCTGAGGGAA
CAGGCCAAAGGCGATGCCACAGAGAACTTTGAGGATGTTGGGCACCCTATACACACCAGAGAATTGTCCAAATCATTCAT
CATCAGGGAGCTGCATCCGGAAGACGGATCAAAGCTGAGCAAGTCCACGTAAACTCTTACCACCACCGTCGATTCTAATT
CCAGCTGGTGGACCAGCTGGGTGATCACAGCCATCTCCGCCCTAGCCCTGCACTCATGCATCAGCTCTACATGGCCCATG
AC

Alignment

ORF - retro_opri_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEQSNQAVKYYTLEEIKKHNHSKSTWLII-HYKVYDLTKFLE-HPGGEEVLREQAGGDATENFEDVGHS
          MAEQ.NQAVKYYTLEEIKKHNHSKS.WLI..H.....LTKFLE.HP.GEEVLREQA.GDATENFEDVGH.
Retrocopy MAEQCNQAVKYYTLEEIKKHNHSKSPWLIT>HKVIIHLTKFLEEHPAGEEVLREQAKGDATENFEDVGHP

Parental  TDARELSKSFIIGELHPDDRSKLSKPTETLITTIDSNSSWWTNWVIPAISALAV-ALMYRLYMADD
          ...RELSKSFII.ELHP.D.SKLSK.T.TL.TT.DSNSSWWT.WVI.AISALA..ALM..LYMA.D
Retrocopy IHTRELSKSFIIRELHPEDGSKLSKST*TLTTTVDSNSSWWTSWVITAISALAL<ALMHQLYMAHD

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_405 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 26 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013614	2 retrocopies	retro_amel_1727, retro_amel_860,
Canis familiaris	ENSCAFG00000000026	2 retrocopies	retro_cfam_32, retro_cfam_787,
Choloepus hoffmanni	ENSCHOG00000000359	2 retrocopies	retro_chof_128, retro_chof_239,
Callithrix jacchus	ENSCJAG00000003163	3 retrocopies	retro_cjac_2427, retro_cjac_2602, retro_cjac_686,
Cavia porcellus	ENSCPOG00000012111	1 retrocopy	retro_cpor_1140,
Equus caballus	ENSECAG00000017581	1 retrocopy	retro_ecab_12,
Erinaceus europaeus	ENSEEUG00000010683	1 retrocopy	retro_eeur_587,
Echinops telfairi	ENSETEG00000000691	1 retrocopy	retro_etel_381,
Homo sapiens	ENSG00000166347	3 retrocopies	retro_hsap_1307, retro_hsap_1373, retro_hsap_2462,
Gorilla gorilla	ENSGGOG00000007968	1 retrocopy	retro_ggor_1068,
Macropus eugenii	ENSMEUG00000015899	1 retrocopy	retro_meug_1573,
Myotis lucifugus	ENSMLUG00000011462	5 retrocopies	retro_mluc_1159, retro_mluc_1333, retro_mluc_1475, retro_mluc_1701, retro_mluc_1908,
Macaca mulatta	ENSMMUG00000013607	3 retrocopies	retro_mmul_2162, retro_mmul_2199, retro_mmul_546,
Mustela putorius furo	ENSMPUG00000016630	1 retrocopy	retro_mputfur_776,
Mus musculus	ENSMUSG00000024646	1 retrocopy	retro_mmus_2177,
Nomascus leucogenys	ENSNLEG00000009232	1 retrocopy	retro_nleu_1066,
Otolemur garnettii	ENSOGAG00000000052	4 retrocopies	retro_ogar_1248, retro_ogar_1888, retro_ogar_2041, retro_ogar_2869,
Ochotona princeps	ENSOPRG00000011584	3 retrocopies	retro_opri_1091, retro_opri_296, retro_opri_405 ,
Pongo abelii	ENSPPYG00000009240	2 retrocopies	retro_pabe_1094, retro_pabe_1140,
Pan troglodytes	ENSPTRG00000010111	3 retrocopies	retro_ptro_1421, retro_ptro_898, retro_ptro_943,
Rattus norvegicus	ENSRNOG00000015205	2 retrocopies	retro_rnor_1565, retro_rnor_2455,
Ictidomys tridecemlineatus	ENSSTOG00000022436	1 retrocopy	retro_itri_1617,
Tupaia belangeri	ENSTBEG00000014998	3 retrocopies	retro_tbel_3229, retro_tbel_3338, retro_tbel_4600,
Tarsius syrichta	ENSTSYG00000002241	1 retrocopy	retro_tsyr_1033,
Tursiops truncatus	ENSTTRG00000015272	1 retrocopy	retro_ttru_1588,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,