RetrogeneDB ID: retro_opri_1019

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_583:85862..86330(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSOPRG00000009229
• Aliases: None
• Description: nucleophosmin/nucleoplasmin 3 [Source:HGNC Symbol;Acc:7931]

Sequence

>retro_opri_1019
GGGAGTGTCGGGACTCCTCGCATCCCGGCCCCAGTCACTATGGACAATTTCTTCTCCGGCTGCTAGCTCTCCGGGCAGAC
ACGCTCTTTCGTCTTCAAAGTGGAGCAAGAGGAGGACGCAGAGCACGTGCTGGTACTGACCATGCTCTGTCTCACTGAGG
GGGCCAAGGAGGAGTGTAGCGTGGTAGAAGTGGTGGCCCAGAGCCATGACCACCAGGAGACTGCAGTCCCTGTGGCCAAC
CTCAGGTTGTCCTGTCAGTCCATGCTCAGCCTGGGTGACTTCCAGCTCCAACCACCTGTCACCTTCCGCCTGAAGTCGTG
CTCTGGCCTTGTGCGCTTCACTGGGCGGCACAAGATTGTTACCATAAGCAATGATGACTCCGAAGAAGAGGAGAGTGAGG
AAGAAGAGAGTGACGGGGAGGATACTGAGCTGTGCCCCATCCTGTCAGCCAAAAAGCAGGGGGCCAGG

Alignment

ORF - retro_opri_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.26 %
• Parental protein coverage: 88.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAVGPLRIPAPVTMDSFFFGCELSGQTRAFTFKVEQEDDAEHVLALTMLCLTEGAKEECNVVEVVARSHD
          G.VG..RIPAPVTMD.FF.GC.LSGQTR.F.FKVEQE.DAEHVL.LTMLCLTEGAKEEC.VVEVVA.SHD
Retrocopy GSVGTPRIPAPVTMDNFFSGC*LSGQTRSFVFKVEQEEDAEHVLVLTMLCLTEGAKEECSVVEVVAQSHD

Parental  HQEIAVPVANLRLSCQPMLSLDDFQLQPPVTFRLKSGSGPVRITGRHQIVTISNDVSEEEESEEEESDGE
          HQE.AVPVANLRLSCQ.MLSL.DFQLQPPVTFRLKS.SG.VR.TGRH.IVTISND.SEEEESEEEESDGE
Retrocopy HQETAVPVANLRLSCQSMLSLGDFQLQPPVTFRLKSCSGLVRFTGRHKIVTISNDDSEEEESEEEESDGE

Parental  DAELCPILPAKKQGGR
          D.ELCPIL.AKKQG.R
Retrocopy DTELCPILSAKKQGAR

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_1019 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019 , retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,