RetrogeneDB ID: retro_opri_1090

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_69840:4849..5291(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLMO2
• Ensembl ID: ENSOPRG00000002550
• Aliases: None
• Description: slowmo homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:15892]

Sequence

>retro_opri_1090
GGGAAGCTCAATAGCCACACTCTCCTCAGCATCAAGTAGGGCCTGCCTTCCATTGTGAAGTTTCCCATCAGTGCAGCAAG
AACCCAAAATGTATGTGCAAAAGCATTCTGTGGTTGATCCTGTAAAAAGAACTATGGAACTCAACTCTGCCAATATTTCA
TTTCCATATATGGTTTCAGCAGATAAGAGGCTTATGTACAAACCACACGCTCAGGACCCAGAAAAAACTGATCTAACTCA
AGAAGCCATAAACATTGTGAAAGGAGTCAGCCTCAGCAGTTACCCGAAAGGACTGTTGGCAAGTACAATGTCTTAGACTG
CTAGTAAGAGCTGAGAACAACGGAGTGGGTGATCCACAATTAAATGCTGAAACTGAAGAACTGGCAGTATTAGCGAGAGG
GAGAAAAGGGCACCAGTGTTGAAAGCTTCATTCACTAAAAAA

Alignment

ORF - retro_opri_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 76.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKLH-HRLLSTEWGLPSIVKSLIGAART-KTYVQEHSVVDPAERVMELNSTNISFTNMVSVDERLLYKPH
          GKL..H.LLS...GLPSIVK..I.AART.K.YVQ.HSVVDP..R.MELNS.NISF..MVS.D.RL.YKPH
Retrocopy GKLNSHTLLSIK*GLPSIVKFPISAART>KMYVQKHSVVDPVKRTMELNSANISFPYMVSADKRLMYKPH

Parental  PQDPGRTVLTQEAIITVKGVSLSSYLEGLMATSISSNANKGRE-AMEWVIR-KLNAELEELAASARG-SL
          .QDP..T.LTQEAI..VKGVSLSSY..GL.A...S..A.K..E...EWVI...LNAE.EELA..ARG...
Retrocopy AQDPEKTDLTQEAINIVKGVSLSSYPKGLLASTMS*TASKS*E<TTEWVIH<QLNAETEELAVLARG<EK

Parental  RAPMAAAAFAEK
          RAP...A.F..K
Retrocopy RAPVLKASFTKK

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_1090 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 12 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018905	4 retrocopies	retro_cjac_1286, retro_cjac_2921, retro_cjac_3171, retro_cjac_3236,
Dasypus novemcinctus	ENSDNOG00000014548	3 retrocopies	retro_dnov_1402, retro_dnov_2032, retro_dnov_2311,
Echinops telfairi	ENSETEG00000009651	3 retrocopies	retro_etel_1130, retro_etel_1262, retro_etel_632,
Loxodonta africana	ENSLAFG00000000300	1 retrocopy	retro_lafr_700,
Myotis lucifugus	ENSMLUG00000014907	2 retrocopies	retro_mluc_1887, retro_mluc_845,
Macaca mulatta	ENSMMUG00000007560	4 retrocopies	retro_mmul_1155, retro_mmul_1644, retro_mmul_2123, retro_mmul_539,
Monodelphis domestica	ENSMODG00000016608	5 retrocopies	retro_mdom_1596, retro_mdom_1619, retro_mdom_1620, retro_mdom_1655, retro_mdom_405,
Mus musculus	ENSMUSG00000016257	2 retrocopies	retro_mmus_2725, retro_mmus_630,
Oryctolagus cuniculus	ENSOCUG00000005621	8 retrocopies	retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Ochotona princeps	ENSOPRG00000002550	8 retrocopies	retro_opri_1069, retro_opri_1090 , retro_opri_141, retro_opri_216, retro_opri_45, retro_opri_663, retro_opri_683, retro_opri_770,
Rattus norvegicus	ENSRNOG00000046644	2 retrocopies	retro_rnor_422, retro_rnor_423,
Sorex araneus	ENSSARG00000004671	2 retrocopies	retro_sara_282, retro_sara_430,