RetrogeneDB ID: retro_opri_1192

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9189:26970..27375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1B2
• Ensembl ID: ENSOPRG00000017163
• Aliases: None
• Description: eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]

Sequence

>retro_opri_1192
GTGGGTTTTGGAGATCTGAAGAGTCCTGCCTGCTGACATGTACTCAGCGACTAACCTGTTGGACAAGAGCTACGTTGAGG
GCTATGTGCCAACACAAGCAGAGGTGGCAGTGTCCGAAGCTGCATTCGGCTGCCACCTGCTCACTTGTGTCATGCCCTCC
GCTGGCAGAATCGCGTCATAAAGGACCAGGAGGAGAAGGCCAGCCTGCTAGGAGGGAGAAGCTTTCGGCAAGTAAAGGCC
CCGTGGATGTGGAAGACACTAAAGGAAGTGAAGGTAGAGAATAAAGAGGATGATGACACTGACCTCTTTGGGTCTAATGA
TGAGGAGGGAAGTGAAGAGGCAAAGAAGCGAAGGGAAGAACTTCCACAGGACGAGTCCAAGACAGCCAAAGAGCCTGCGG
CTGTT

Alignment

ORF - retro_opri_1192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.99 %
• Parental protein coverage: 86.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGFGDLKSPAGLQVLND-YLADKSYIEGYVPSQADVAVFEAVSS-PPPGDLCHALRWYNHIKSYEKEKAS
          .GFGDLKSPA...VL.D..L.DKSY.EGYVP.QA.VAV.EA.....PP..LCHALRW.N.......EKAS
Retrocopy VGFGDLKSPAC*HVLSD>NLLDKSYVEGYVPTQAEVAVSEAAFG<LPPAHLCHALRWQNRVIKDQEEKAS

Parental  LPGVK-KALGKYGPADVEDTTGSGGTD-GKDDDDIDLFGSDDEEESEEAKKLREERLAQYESKKAKKPAL
          L.G...K.....GP.DVEDT.GS.G.....DD.D.DLFGS.DEE.SEEAKK.REE.L.Q.ESK.AK.PA.
Retrocopy LLGGR<KLSASKGPVDVEDTKGSEGRE>KEDD-DTDLFGSNDEEGSEEAKKRREE-LPQDESKTAKEPAA

Parental  V
          V
Retrocopy V

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_1192 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 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029635	1 retrocopy	retro_cfam_56,
Callithrix jacchus	ENSCJAG00000005805	2 retrocopies	retro_cjac_176, retro_cjac_341,
Cavia porcellus	ENSCPOG00000014496	4 retrocopies	retro_cpor_1116, retro_cpor_1381, retro_cpor_1407, retro_cpor_296,
Gorilla gorilla	ENSGGOG00000007002	2 retrocopies	retro_ggor_134, retro_ggor_2000,
Macropus eugenii	ENSMEUG00000002654	8 retrocopies	retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Myotis lucifugus	ENSMLUG00000016602	8 retrocopies	retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Oryctolagus cuniculus	ENSOCUG00000009848	4 retrocopies	retro_ocun_1014, retro_ocun_1240, retro_ocun_544, retro_ocun_922,
Oreochromis niloticus	ENSONIG00000017630	1 retrocopy	retro_onil_28,
Ochotona princeps	ENSOPRG00000017163	3 retrocopies	retro_opri_1192 , retro_opri_294, retro_opri_748,
Oryzias latipes	ENSORLG00000018533	1 retrocopy	retro_olat_16,
Pongo abelii	ENSPPYG00000013107	7 retrocopies	retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389, retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Sarcophilus harrisii	ENSSHAG00000017853	1 retrocopy	retro_shar_208,
Ictidomys tridecemlineatus	ENSSTOG00000005437	3 retrocopies	retro_itri_1263, retro_itri_813, retro_itri_873,
Xiphophorus maculatus	ENSXMAG00000006050	1 retrocopy	retro_xmac_21,