RetrogeneDB ID: retro_opri_500

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_141197:113..630(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000008216
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSOPRG00000005085
• Aliases: None
• Description: ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]

Sequence

>retro_opri_500
ATGTTCACCTCCGGTGCCAAGATCATGAAGCCAAACAGCGAGAAGCCGAGTGAGTTCAAGCCGGGCATCTTTCAGGCACT
GCTGGGCTGGAGATGAACTCAGACCCAAAAGCTCAGCTAAGGGAGCTAAACACCATGGCCACCAAGGAAACGGAAGTTGG
TGGTGGCCAGAAAGCTATCATAATCTGTGTGCCTGTCCCTCAACTGAAACACTTCCAGAAGATTCAAGTCTTGGCTAGTG
TATGAATTGGAGAAAAAGTTTAGTGGTAAGCACGTTGTCTGTATTGCTCGGAGGAGAAAGCTGCCCAAGTCAACTCGGAA
AAGCCGCCTGAAAAGAACAAGCAGAGAAGCGTCCCGGGAGCCGCACCGACAGCTGCGCACCTGCAGTCTTTGAGGATCTG
GGCTTCCCAAGTGACGCCATGGGCAAAGCACCCGCGGCAAGCTGGATGGCAGCCACCTCCTGCAGATTTCATCTGGGCAA
AGTACAGCAGAAAAACGTGGAGCATAAGTTGGAAACT

Alignment

ORF - retro_opri_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.86 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEFESGISQALLE-LEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQL
          MF.S.AKI.KPN.EKP.EF..GI.QALL..LEMNSD.KAQLRELN..A.KE.EVGGG.KAIII.VPVPQL
Retrocopy MFTSGAKIMKPNSEKPSEFKPGIFQALLG<LEMNSDPKAQLRELNTMATKETEVGGGQKAIIICVPVPQL

Parental  KSVQKTQVR-LVRELEKKLSGK--VFMAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSE
          K..QK.QV..LV.ELEKK.SGK..V..A.RR.LPK.TRKSR.K..................L.....P..
Retrocopy KHFQKIQVL>LVYELEKKFSGKHVVCIARRRKLPKSTRKSRLKRTSREASREPHRQLRTCSL*GSGLPK*

Parental  IVGKRIRVKLDGSRLIKV-HLDKAQQNNVEHKVET
          ..G...R.KLDGS.L....HL.K.QQ.NVEHK.ET
Retrocopy RHGQSTRGKLDGSHLLQI>HLGKVQQKNVEHKLET

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_500 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 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Ochotona princeps	ENSOPRG00000005085	3 retrocopies	retro_opri_1036, retro_opri_415, retro_opri_500 ,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,