RetrogeneDB ID: retro_opri_943

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4822:30782..32025(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNPLA8
• Ensembl ID: ENSOPRG00000006448
• Aliases: None
• Description: patatin-like phospholipase domain containing 8 [Source:HGNC Symbol;Acc:28900]

Sequence

>retro_opri_943
CAGGCGCTGAGAAGAACATCTGACCCAAAGCTCTGCATCACAAGGGTAGAAGAGCTGACTTTCCATCTTCTCGAATTTCC
TGAAGGAAAAGGAGTGGCTGCGAAGGAAAGAATTATTCCTTATTTATTGTGACTGAGGCAAATGAAGGATGAAACTCTTC
AGGCTGCAGTTAGAGAAATTTTGGCCTTGATTGGTTATGTGGATCCAGTGAAAGGCAGAGGGATTCGAATTCTTACAATT
GATGGTGGAGGAACAAGGGGTGTGGTTGCTCTTCAGACGCTCAGAAAATTAGTTGAACTTACTCAGAAGCCAGTTCATCA
GCTCTTTGATTACATCTGTGGTGTAAGCATAGGTGACATATTAGCTTTCATGTTAGGACTGTTCCACATGCCACTGGACG
AATGTGAGGAACTTTATCGGAAACTAGGATCAGATGTATTTTCACAAATGTCATCGTTGGAACAGTCAAAATGAGCTGGA
GCCATGCATTTTATGACAGTCAGACATGGGAAAAGATTCTTAAGGAGAGAATGGGATCTGCACTAATGATTGAAACAGCA
AGAAACCCCACGTGTCCTAAGGTAGCTGCTGTGAGTACTATCGTAAACAGAGGGATAACGCCAAAAGATTTTGTGTTCAG
AAACTATGGTCATTTTCCTGGAATCAAGTCTCATTACTTGGGAGGCTGTCAGTACAAGATGTGGCAGGCCATCAGAGCCT
CCTCTGCTGCCCCGGGCTACTTTGCAGAATACACCCTGGGAAACGATCTGCATCAGGATGGAGGTTTGCTTCTGAATAAC
CCTTTGGCATTGGCAATGCATGAGTGTAAGTGCCTTTGGCCAGACGTCCCGCTGGAGTGCATTGTTTCCCGGGCACTGGC
TGCTATGACAGCGATGTGAGGAACACTGCAACATACACAAGCCTGAAAACCAAACTTTCTAATGTCATCAACAGTGCTAC
CGACACAGAAGAGGTCCATATTATGCTGGATGGTCTGTTACCTCCTGACACCTACTTCAGATTCAATCCTGTCATGTGTG
AGAACATACCTCTGGATGAAAGTCGAAATGAAAAACTGGATCAGCTGCAGCTGGAGGGCTCCAAGTACATAGAAAGAAAT
GAGCAAAAAATGAAAAAAGTTGCAAAAATCCTGAGTCAAGAAAAAACAACCCTGCAGAAAATCAACGATTGGATCAAATT
AAAAACTGACATGTATGAAGGCCTTCCGTTCTTTTCAAAATTA

Alignment

ORF - retro_opri_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAFTRTT--KLCFTRVEELTFHLFEFHEGKGAAAKERIIPYLLRLRQMKDETLQAAVREILALIGYVDPV
          QA..RT...KLC.TRVEELTFHL.EF.EGKG.AAKERIIPYLL.LRQMKDETLQAAVREILALIGYVDPV
Retrocopy QALRRTSDPKLCITRVEELTFHLLEFPEGKGVAAKERIIPYLL*LRQMKDETLQAAVREILALIGYVDPV

Parental  KGRGIRILTIDGGGTRGVVALQTLRKLVELTQKPVHQLFDYICGVSTGAILAFMLGLFHMPLDECEELYR
          KGRGIRILTIDGGGTRGVVALQTLRKLVELTQKPVHQLFDYICGVS.G.ILAFMLGLFHMPLDECEELYR
Retrocopy KGRGIRILTIDGGGTRGVVALQTLRKLVELTQKPVHQLFDYICGVSIGDILAFMLGLFHMPLDECEELYR

Parental  KLGSDVFSQ-NVIVGTVKMSWSHAFYDSQTWEKILKERMGSALMIETARNPTCPKVAAVSTIVNRGITPK
          KLGSDVFSQ.NVIVGTVKMSWSHAFYDSQTWEKILKERMGSALMIETARNPTCPKVAAVSTIVNRGITPK
Retrocopy KLGSDVFSQ<NVIVGTVKMSWSHAFYDSQTWEKILKERMGSALMIETARNPTCPKVAAVSTIVNRGITPK

Parental  AFVFRNYGHFPGIKSHYLGGCQYKMWQAIRASSAAPGYFAEYALGNDLHQDGGLLLNNPSALAMHECKCL
          .FVFRNYGHFPGIKSHYLGGCQYKMWQAIRASSAAPGYFAEY.LGNDLHQDGGLLLNNP.ALAMHECKCL
Retrocopy DFVFRNYGHFPGIKSHYLGGCQYKMWQAIRASSAAPGYFAEYTLGNDLHQDGGLLLNNPLALAMHECKCL

Parental  WPDVPLECIVSL-GTGRYESDVRNTATYTSLKTKLSNVINSATDTEEVHIMLDGLLPPDTYFRFNPVMCE
          WPDVPLECIVS..GTG.Y.SDVRNTATYTSLKTKLSNVINSATDTEEVHIMLDGLLPPDTYFRFNPVMCE
Retrocopy WPDVPLECIVSR<GTGCYDSDVRNTATYTSLKTKLSNVINSATDTEEVHIMLDGLLPPDTYFRFNPVMCE

Parental  NIPLDESRNEKLDQLQLEGSKYIERNEQKMKKVAKILSQEKTTLQKINDWIKLKTDMYEGLPFFSKL
          NIPLDESRNEKLDQLQLEGSKYIERNE...............TLQKINDWIKLKTDMYEGLPFFSKL
Retrocopy NIPLDESRNEKLDQLQLEGSKYIERNEXXXXXXXXXXXXXXXTLQKINDWIKLKTDMYEGLPFFSKL

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_943 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000006448	2 retrocopies	retro_opri_341, retro_opri_943 ,