RetrogeneDB ID: retro_opri_746

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_27721:5860..6136(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSOPRG00000005086
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]

Sequence

>retro_opri_746
GCGGCCGCGGCCAGTGTGGGCCAGCTAAAAGAGGAGGCTCTGCAGCGAAAGAAAAGGCTGAGGGCCCTGCAGGAGAAAGC
CGGACACAAGGACAAGGAAGACGGGGAACCCAAGACCAAGCGGCTCAGAGTGGAGGAAGAAGACGAGAAGCCGAGGGAAC
TCGGGCTGCAGAATTATGTCCCAGAGGATGAGGACCTGGAGAGCAGGAGGGTACCCCCGATCGAGCCAGTCATGGAGGAA
GTGAACCCAGCCAACCTCGCTCCCTGGAAGCCTGAC

Alignment

ORF - retro_opri_746 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.37 %
• Parental protein coverage: 56.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAGVGRLEEEALRRKERLRALREKTGRKDKQEGELKAKQPREEEEGEKHRELRLRNYVPEDEDLKRRR
          AAAA.VG.L.EEAL.RK.RLRAL.EK.G.KDK..GE.K.K..R.EEE.EK.REL.L.NYVPEDEDL..RR
Retrocopy AAAASVGQLKEEALQRKKRLRALQEKAGHKDKEDGEPKTKRLRVEEEDEKPRELGLQNYVPEDEDLESRR

Parental  VPQAKPVAVEEKVKEQLEAAKPE
          VP...PV..EE.....L...KP.
Retrocopy VPPIEPV-MEEVNPANLAPWKPD

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_746 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746 ,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,