RetrogeneDB ID: retro_opri_1002

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_55557:9152..9517(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD4
• Ensembl ID: ENSOPRG00000015147
• Aliases: None
• Description: RWD domain containing 4 [Source:HGNC Symbol;Acc:23750]

Sequence

>retro_opri_1002
TTTCATTTCAATACAGGATCATCAGCTGCAAAGCAGAGTATATTGGCCAAGTTACAGGAAGCAGTAGAGGTGAACCTGGG
CACTGCCATGACCTATACAATGTTTAAGTATGCCAAGGACAATGAAGAGCAGTTCTTGGAGAATCATCATCCCATCACTT
CCACTACGTCCACAAGTACTGTAATCTCAACTGAAACTCCGAATACAGCCCCATCAAGCAAGAAAAAACACAAAAAAGAA
CAGCTTTCAAAAGCCCACAAACGTAAGCTGGCAGACAAAACAGACCACAAAGGGGAACCCCCTCGAGGCTGGAGCTGGGT
CCATGTCATGAAGCATTTAAGCAAACTGGCTCAAAAGATGATGAA

Alignment

ORF - retro_opri_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFNNTISSAVKQSILAKLQEAVEVNLGTAMTYTLFEYAKDNKEQFMEHHHPITSTTSTSNIISTETPNTA
          F..NT.SSA.KQSILAKLQEAVEVNLGTAMTYT.F.YAKDN.EQF.E.HHPITSTTSTS..ISTETPNTA
Retrocopy FHFNTGSSAAKQSILAKLQEAVEVNLGTAMTYTMFKYAKDNEEQFLENHHPITSTTSTSTVISTETPNTA

Parental  PSSKKKDKKEQLSKAQKRKLADKTXXXXXXXXXXXXXXXXXHLSK-TGSKDDE
          PSSKKK.KKEQLSKA.KRKLADKT.................HLSK.TGSKDDE
Retrocopy PSSKKKHKKEQLSKAHKRKLADKTDHKGEPPRGWSWVHVMKHLSK<TGSKDDE

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_1002 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 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003081	1 retrocopy	retro_btau_603,
Canis familiaris	ENSCAFG00000007880	1 retrocopy	retro_cfam_1281,
Choloepus hoffmanni	ENSCHOG00000005290	3 retrocopies	retro_chof_1477, retro_chof_441, retro_chof_887,
Dasypus novemcinctus	ENSDNOG00000015132	1 retrocopy	retro_dnov_968,
Felis catus	ENSFCAG00000024337	1 retrocopy	retro_fcat_1156,
Homo sapiens	ENSG00000182552	2 retrocopies	retro_hsap_3770, retro_hsap_3841,
Gorilla gorilla	ENSGGOG00000011982	1 retrocopy	retro_ggor_2536,
Myotis lucifugus	ENSMLUG00000006800	1 retrocopy	retro_mluc_545,
Monodelphis domestica	ENSMODG00000004223	2 retrocopies	retro_mdom_1015, retro_mdom_251,
Nomascus leucogenys	ENSNLEG00000010733	1 retrocopy	retro_nleu_1898,
Otolemur garnettii	ENSOGAG00000016709	5 retrocopies	retro_ogar_1084, retro_ogar_1171, retro_ogar_1228, retro_ogar_2652, retro_ogar_2789,
Ochotona princeps	ENSOPRG00000015147	1 retrocopy	retro_opri_1002 ,
Pongo abelii	ENSPPYG00000015230	1 retrocopy	retro_pabe_3082,
Pan troglodytes	ENSPTRG00000016632	2 retrocopies	retro_ptro_1456, retro_ptro_2556,
Rattus norvegicus	ENSRNOG00000022500	1 retrocopy	retro_rnor_2930,
Sarcophilus harrisii	ENSSHAG00000011971	1 retrocopy	retro_shar_760,
Sus scrofa	ENSSSCG00000015776	2 retrocopies	retro_sscr_1019, retro_sscr_1051,
Ictidomys tridecemlineatus	ENSSTOG00000013086	1 retrocopy	retro_itri_533,
Tarsius syrichta	ENSTSYG00000006599	1 retrocopy	retro_tsyr_1898,
Vicugna pacos	ENSVPAG00000005743	1 retrocopy	retro_vpac_341,