RetrogeneDB ID: retro_opri_496

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_14025:43768..44229(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000012667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSOPRG00000005487
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_opri_496
ACTGGGCCCGGGGATGCCCGAGGAAAGGGAGCCGATGCCAAGGAGGTAAAAGCCGCAGTAGAGCCACTCCGAGTACCTCC
ACCATGCAAACTGACATCTGTTACCGCTGTGGTGAGTCTGGTCATTATGCCAAAAACTGTAACCTTCTCGAAAACATCTG
CTACAACTGTGGGAGGACTGGCCACATCGCCAAGGATTGTCTGGAGCCTAAACGTGAGAAAGATCAGTGCTGTTACATCT
GCGGCCGAATGGGTCATCTGTCTCGTGATTGCACCCATCTAGAAGAACAGAAATGCTATTCTTGCGGTGAATTTGGGCAC
TTCCAGAAAGACTGCACCCAAGTTAAGTGCTATCGATGTGGCGAGAATGGACACGTGGCCATCAACTGCCATAAGGGAAG
CAAAATGAACTGTTACCGGTGTGGTAGGTTTGGACATTTAGCCCGAGACTGTAAGAACGAG

Alignment

ORF - retro_opri_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.74 %
• Parental protein coverage: 87.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGGGRGRGMR-SRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKE
          TG.G..RG...SR..GG....R.....S....DICYRCGESGH.AK.C.L.E..CYNCGR.GHIAKDC.E
Retrocopy TGPGDARGKG<SRCQGGKSRSRATPSTSTMQTDICYRCGESGHYAKNCNLLENICYNCGRTGHIAKDCLE

Parental  PKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCY
          PKRE..QCCY.CG..GHL.RDC.H..EQKCYSCGEFGH.QKDCT.VKCYRCGE.GHVAINC.K.S..NCY
Retrocopy PKREKDQCCYICGRMGHLSRDCTHLEEQKCYSCGEFGHFQKDCTQVKCYRCGENGHVAINCHKGSKMNCY

Parental  RCGESGHLARECTIE
          RCG..GHLAR.C..E
Retrocopy RCGRFGHLARDCKNE

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_496 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015334	2 retrocopies	retro_amel_1285, retro_amel_1773,
Canis familiaris	ENSCAFG00000004320	2 retrocopies	retro_cfam_1272, retro_cfam_23,
Cavia porcellus	ENSCPOG00000012816	2 retrocopies	retro_cpor_424, retro_cpor_94,
Dipodomys ordii	ENSDORG00000002919	1 retrocopy	retro_dord_569,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Homo sapiens	ENSG00000169714	1 retrocopy	retro_hsap_50,
Gorilla gorilla	ENSGGOG00000010085	1 retrocopy	retro_ggor_2926,
Macropus eugenii	ENSMEUG00000011699	1 retrocopy	retro_meug_55,
Myotis lucifugus	ENSMLUG00000012554	1 retrocopy	retro_mluc_141,
Macaca mulatta	ENSMMUG00000011585	1 retrocopy	retro_mmul_2505,
Mustela putorius furo	ENSMPUG00000017315	3 retrocopies	retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus	ENSMUSG00000030057	1 retrocopy	retro_mmus_230,
Nomascus leucogenys	ENSNLEG00000014482	1 retrocopy	retro_nleu_1986,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Ochotona princeps	ENSOPRG00000005487	5 retrocopies	retro_opri_139, retro_opri_49, retro_opri_496 , retro_opri_566, retro_opri_965,
Pongo abelii	ENSPPYG00000013423	1 retrocopy	retro_pabe_3658,
Pan troglodytes	ENSPTRG00000015369	1 retrocopy	retro_ptro_3131,
Rattus norvegicus	ENSRNOG00000010239	2 retrocopies	retro_rnor_207, retro_rnor_727,
Ictidomys tridecemlineatus	ENSSTOG00000000173	1 retrocopy	retro_itri_113,
Tarsius syrichta	ENSTSYG00000004344	1 retrocopy	retro_tsyr_1889,
Vicugna pacos	ENSVPAG00000007138	1 retrocopy	retro_vpac_548,