RetrogeneDB ID: retro_opri_735

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2699:46829..47351(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL4
• Ensembl ID: ENSOPRG00000007792
• Aliases: None
• Description: ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]

Sequence

>retro_opri_735
GGCCCTTCCATCAACTACAATAAGGACACTGGTGTCAGGAAGGCCTGCAGAGACCTTCCAGAAATCACTTCACTACTGTA
AGCAGACTGAATACTCTGACACTGGCTCTTAGTGGGTATGTGGGCTGCATCTGCATTTGGACTGAAAGTGTTTTCTGGAA
GCTAGCTGAAGTGTGTGGCGCTTGGCACAAGGCGCTTCTCTCAAGAGTTTCCACATGTTTCCTAGGCACAGGATGATCCA
AACAGACCGTTCCAGGAACGTGGAAAGCCCACGTATCCCAGGCACCCTCCCAGCACCACACAAGAAATGGATCACCCAAT
CCTGAAGAAGAATCCAACGAAAAACCTGACAATCATGCCAAGGGTGATGCCATATTGCAACACCATGTGCCAAACCATTA
TTTATCAAGCCAGAAATCACAAACCCTGGGTAGAGGAGGCAGCAGCAGCTCTGGCAGCCAAATCAGATGAGAAGCGGATC
GCAGGCTGGAAGCCTGTGGTAGGGAAGCAAGGAGAGAAGGCT

Alignment

ORF - retro_opri_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.75 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPCIIYNEDNGIIKAFRNIPGITLL-NVSKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKA-ASL
          GP.I.YN.D.G..KA.R..P.IT.L..VS.LN.L.LA..G.VG..CIWTES.F.KL....G.W.KA.ASL
Retrocopy GPSINYNKDTGVRKACRDLPEITSL<TVSRLNTLTLALSGYVGCICIWTESVFWKLAEVCGAWHKA<ASL

Parental  KSNYNLPMHKMLNTDLSRILKSPEIQRALRAPRKK-IHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILR
          KS....P.H.M..TD.SR...SP.I...L.AP.KK......LKKNP.KNL.IM....PY..TM...TI..
Retrocopy KSFHMFPRHRMIQTDRSRNVESPRIPGTLPAPHKK<MDHPILKKNPTKNLTIMPRVMPYCNTMCQ-TIIY

Parental  QARNHKLRVERAAAVLAAKSDKKEGADKKPVVLKKVKKS
          QARNHK..VE.AAA.LAAKSD.K..A..KPVV.K...K.
Retrocopy QARNHKPWVEEAAAALAAKSDEKRIAGWKPVVGKQGEKA

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_735 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 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Cavia porcellus	ENSCPOG00000003055	1 retrocopy	retro_cpor_370,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Mus musculus	ENSMUSG00000032399	2 retrocopies	retro_mmus_2863, retro_mmus_495,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Oryctolagus cuniculus	ENSOCUG00000008794	3 retrocopies	retro_ocun_1134, retro_ocun_630, retro_ocun_631,
Ochotona princeps	ENSOPRG00000007792	1 retrocopy	retro_opri_735 ,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,