RetrogeneDB ID: retro_opri_552

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_16861:49476..49859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX1
• Ensembl ID: ENSOPRG00000003699
• Aliases: None
• Description: chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]

Sequence

>retro_opri_552
TTCTCAAATGAGGACAGTGCTTTGGGAACCAGAAGAGAATCTGCATGGAGTTGACCTCACTGATGCGTCCCTCAGTCCCA
AAGAATAGCACATGAGACTCAGTAGTCAGAGGGCGGCTGGCACAAAGTTGATTCTGATTCTGAAGATTAGGGAAAGGAGA
GCAAACCAAAGAACAAAGGAGAGTCATAAAAGCCACCAGATTTTGCTTGAGGGTTATAGTCAAAACAGATTATTGCAGCC
ACAGATTCCAGTGGAGAACTCATGTCTCTGAGGAAATGGAAAACTCCGACAAGGCTGAGCTGCTCCCTGCCAAGGAAGCC
AATGTTGTGTTCCGACAGGTTGCCATGTCCTTCCAAGAGGAAAGTGATACACAGGCAGATTAT

Alignment

ORF - retro_opri_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.12 %
• Parental protein coverage: 69.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FSDEDNT-WEPEENLDCPDLIAEFL-QSQKTAHETDKSEGGKRKADSDSEDKGEESKPKKKKEESEKPRG
          FS.ED...WEPEENL...DL....L.QSQ..AHET..SEGG..K.DSDSED.G.ESKP.K.K.ES.KP..
Retrocopy FSNEDSA>WEPEENLHGVDLTDASL<QSQRIAHETQ*SEGGWHKVDSDSED*GKESKP-KNKGES*KPPD

Parental  FARGLEPERIIGATDSSGELMFLMKWK-NSDEADLVPAKEANVKCPQVVISFYEERLTWHSY
          FA.GL....II.ATDSSGELM.L.KWK.NSD.A.L.PAKEANV...QV..SF.EE..T...Y
Retrocopy FA*GL*SKQIIAATDSSGELMSLRKWK<NSDKAELLPAKEANVVFRQVAMSFQEESDTQADY

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_552 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.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004890	2 retrocopies	retro_amel_1228, retro_amel_54,
Bos taurus	ENSBTAG00000002949	9 retrocopies	retro_btau_1121, retro_btau_1394, retro_btau_148, retro_btau_1583, retro_btau_1615, retro_btau_550, retro_btau_558, retro_btau_714, retro_btau_807,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Dipodomys ordii	ENSDORG00000000716	2 retrocopies	retro_dord_594, retro_dord_709,
Erinaceus europaeus	ENSEEUG00000004874	3 retrocopies	retro_eeur_121, retro_eeur_228, retro_eeur_396,
Echinops telfairi	ENSETEG00000000203	7 retrocopies	retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Myotis lucifugus	ENSMLUG00000005030	2 retrocopies	retro_mluc_1000, retro_mluc_1533,
Mus musculus	ENSMUSG00000018666	1 retrocopy	retro_mmus_3108,
Oryctolagus cuniculus	ENSOCUG00000008021	3 retrocopies	retro_ocun_177, retro_ocun_442, retro_ocun_55,
Otolemur garnettii	ENSOGAG00000005658	9 retrocopies	retro_ogar_1087, retro_ogar_1092, retro_ogar_1322, retro_ogar_2056, retro_ogar_2396, retro_ogar_2443, retro_ogar_2840, retro_ogar_2880, retro_ogar_368,
Ochotona princeps	ENSOPRG00000003699	1 retrocopy	retro_opri_552 ,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Rattus norvegicus	ENSRNOG00000008689	2 retrocopies	retro_rnor_2388, retro_rnor_2841,
Sarcophilus harrisii	ENSSHAG00000008192	1 retrocopy	retro_shar_76,
Ictidomys tridecemlineatus	ENSSTOG00000023986	3 retrocopies	retro_itri_1282, retro_itri_1599, retro_itri_1867,
Tarsius syrichta	ENSTSYG00000004769	2 retrocopies	retro_tsyr_1672, retro_tsyr_467,