RetrogeneDB ID: retro_opri_888

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4123:143091..143376(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLRB1
• Ensembl ID: ENSOPRG00000004714
• Aliases: None
• Description: dynein, light chain, roadblock-type 1 [Source:HGNC Symbol;Acc:15468]

Sequence

>retro_opri_888
GCAGAGGTGGAGGAGACACTAACATGACTTCAGAGGCAAAGGGGGAGTGCAAGGGATCATTGTGATGAACACAGAGGAAA
TTCCCATCACAAGCACGAGGGATATTCCACCACCACACAGCATGCCAACATTATGCATGCCTTCATCTTGAAGGCACCAA
GCACCACACGTGGAATCAACCTCCAGAATGATCACACCTTTCTTTGAATTTACTTAAAGAAAAGTGAAATTGCATTTGCA
CCAGATAAAGACCATTTTCTGACTGTGATTCAGAATCAAAATGAA

Alignment

ORF - retro_opri_888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.07 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEVEETLKRLQSQK-GVQGIIVVNTEGIPIKSTMDNP-TTTQYANLMHNFILKARSTVREIDPQNDLTFL
          AEVEETL..LQ.Q..GVQGIIV.NTE.IPI.ST.D.P.TTTQ.AN.MH.FILKA.ST.R.I..QND.TFL
Retrocopy AEVEETLT*LQRQR>GVQGIIVMNTEEIPITSTRDIP<TTTQHANIMHAFILKAPSTTRGINLQNDHTFL

Parental  RIRSKKNEIMVAPDKDYFLIVIQNPTE
          .I..KK.EI..APDKD.FL.VIQN..E
Retrocopy *IYLKKSEIAFAPDKDHFLTVIQNQNE

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_888 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 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018199	10 retrocopies	retro_cjac_1010, retro_cjac_1172, retro_cjac_1274, retro_cjac_1539, retro_cjac_2071, retro_cjac_2902, retro_cjac_3185, retro_cjac_3215, retro_cjac_3260, retro_cjac_882,
Equus caballus	ENSECAG00000008404	2 retrocopies	retro_ecab_102, retro_ecab_553,
Echinops telfairi	ENSETEG00000018637	2 retrocopies	retro_etel_218, retro_etel_699,
Homo sapiens	ENSG00000125971	2 retrocopies	retro_hsap_1946, retro_hsap_948,
Gorilla gorilla	ENSGGOG00000023900	1 retrocopy	retro_ggor_764,
Macaca mulatta	ENSMMUG00000031253	1 retrocopy	retro_mmul_779,
Nomascus leucogenys	ENSNLEG00000010082	2 retrocopies	retro_nleu_1478, retro_nleu_2456,
Oryctolagus cuniculus	ENSOCUG00000021027	2 retrocopies	retro_ocun_351, retro_ocun_745,
Otolemur garnettii	ENSOGAG00000016802	2 retrocopies	retro_ogar_7, retro_ogar_983,
Ochotona princeps	ENSOPRG00000004714	1 retrocopy	retro_opri_888 ,
Pongo abelii	ENSPPYG00000010937	1 retrocopy	retro_pabe_810,
Pan troglodytes	ENSPTRG00000013416	1 retrocopy	retro_ptro_655,
Rattus norvegicus	ENSRNOG00000025715	1 retrocopy	retro_rnor_1883,