RetrogeneDB ID: retro_opri_1084

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_68238:3478..4801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0753
• Ensembl ID: ENSOPRG00000000497
• Aliases: None
• Description: KIAA0753 [Source:HGNC Symbol;Acc:29110]

Sequence

>retro_opri_1084
ATGTCTAGGCTGGCAGCTGCCCACCGAGGAGCCGTTCGGGCCTTGCAGATGTTTGTCACCCAGTTTACTGACCGAGGGGA
GCACCCCATTCCTGCCCGCTGTAAGGAGCGGGGAAGCCTTATTCGCCAGCTTTCACTTTGTTCTGCCAAACTGGATGCGC
ATTCTTATGTCCTGATGTGGTTACTGATATTCTGCAACAAATTGAGGCTTTGGAATCTCTCCTGGAAAAGAAACTGTCAC
CAAAAAAGGTGAAGAAATGTGTCGGTGACAGGCGAAGCCGATTTCCAATTGGAAGCCAAAGGACCTTCGCAACATGGCCA
AGCCCATCACCTAAGAATGAACGGAGGCCCTTTGTGGAAAAGGAGATAGTTCCACAGGACACAGGGCTGCCTGCAGTGGC
ACAGAAGCTTCTGGCTGATAAGCACAGGCCTGGCCAAGACTTTCCCATGGCACAGAGGTCGGAGAGAGCTTGAGCCGTTA
GATGCGGATATCGCTCTGGAGCAAGCCCCGTTCATCCTAGATCAGAGTCCAAGGCGCGGGAACAAGGCTTCGGCCCTGCC
AAAAGCCAGAGTAGCCACCAAGAAGCCTGCGGCAGAGAATGTGCCACTGAGGAGGAAGGATGCTCTGGCCCCCGCAAGAC
CGCAGAGCTTCCACAAACCTGAAAGAACCAAGCTGATAAGCCAGCCTCCCAACAAAAGCAGGTTGCAACAGGCAACAGTT
TCACCCCGATTGAAAATGAAGCAGCAGCCTGTGAAAGACGGCCGGGCTCCCTGGGTCCCCCCAAACCCCACGTCCGCGCC
AGCGTCTCCCAAATGCGCCACGTGGCGGAAGATGAGGTCCAGCCCCAGAGGAGCTGCCAAAGAGTAAGGTGTGCAGCAAG
AAGACACTCCAGAGCAAAATCAGTGGAGAGGAGATGTTGAGCACGAAGCAGCCAGGCTCGCTTGGCTTGATGCTGAAACT
TCTAAAAGATTGAAGGAGCTAGAAGAACTAAAAGCCAAAGAAATAAACAAAATGCAAAAACAGAGGCTTGAGTGGCTTGG
TGCTGAAACTTCTAGAAGAACAAAGGAACTGAATGAACTGAGAACCGAAGAAATGGATAGACTCCAAAAACTAAGCATTT
CTGCCACCCAGTTAGCAGACAAGGTGGAGGCGGCAGTTCTGCAGCGTTTGAAGCCTCTCTTGTTGAAGGCCCAGAGAGCT
GGCTCTTCAAGGAAGCAACTGCTCAGCTGAAGGGTTACCTCGCAGGGACACGTGACAGCCCAGCTGCGAGAGCTACAGCT
CTTGATTCTGAGGCAACACGTTCATCAGCTGGATGATTTTCTG

Alignment

ORF - retro_opri_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSRLAAAHRGAIRALQMFVTQFTDRGEHPIPARCKELGSLIRQLSLCSAKLDADSSV-PDVVIDILQQIE
          MSRLAAAHRGA.RALQMFVTQFTDRGEHPIPARCKE.GSLIRQLSLCSAKLDA.S.V.PDVV.DILQQIE
Retrocopy MSRLAAAHRGAVRALQMFVTQFTDRGEHPIPARCKERGSLIRQLSLCSAKLDAHSYV<PDVVTDILQQIE

Parental  ALESLLEKKLSPKKVKKCVGDSRSRFPIGSQRTFATWPSPSPKNERRPFVEKEIVPQDTGLPAVAQKLLA
          ALESLLEKKLSPKKVKKCVGD.RSRFPIGSQRTFATWPSPSPKNERRPFVEKEIVPQDTGLPAVAQKLLA
Retrocopy ALESLLEKKLSPKKVKKCVGDRRSRFPIGSQRTFATWPSPSPKNERRPFVEKEIVPQDTGLPAVAQKLLA

Parental  DKHQPGQD-FPMAQRSERELEALDVDIALEQAPFILDQSPRCGNEASALPKARVATKKPAAENVPLRRKD
          DKH.PGQD.FP...R..RELE.LD.DIALEQAPFILDQSPR.GN.ASALPKARVATKKPAAENVPLRRKD
Retrocopy DKHRPGQD>FPW-HRGRRELEPLDADIALEQAPFILDQSPRRGNKASALPKARVATKKPAAENVPLRRKD

Parental  ALAPARPQQSLHKPERTKLISQPPSKSRLQQATVSSRLKMKQQPVKDSRAPWIPPNPTSPPASPKCAAWR
          ALAPARPQ.S.HKPERTKLISQPP.KSRLQQATVS.RLKMKQQPVKD.RAPW.PPNPTS.PASPKCA.WR
Retrocopy ALAPARPQ-SFHKPERTKLISQPPNKSRLQQATVSPRLKMKQQPVKDGRAPWVPPNPTSAPASPKCATWR

Parental  KVKSSPRGAAKEQGLQQEDTPEQKQWR-DVEHEAARLAWLDAETSKRLKELEELKAKEMNKMQKQRLEWL
          K..SSPRGAAKE.G.QQEDTPEQ.QWR.DVEHEAARLAWLDAETSKRLKELEELKAKE.NKMQKQRLEWL
Retrocopy KMRSSPRGAAKE*GVQQEDTPEQNQWRGDVEHEAARLAWLDAETSKRLKELEELKAKEINKMQKQRLEWL

Parental  GAETSRRTKELNELRTEEMDRLQKLSISATQLADKVEEAVLERLKPLLLKAQRAGSS-EEATAQLKDYLA
          GAETSRRTKELNELRTEEMDRLQKLSISATQLADKVE.AVL.RLKPLLLKAQRAGSS..EATAQLK.YLA
Retrocopy GAETSRRTKELNELRTEEMDRLQKLSISATQLADKVEAAVLQRLKPLLLKAQRAGSS<KEATAQLKGYLA

Parental  GDTVTAQPAEEATALDSE-GN-NVHQLDDFL
          G......PA..ATALDSE.GN..VHQLDDFL
Retrocopy G--TRDSPAARATALDSE<GN<HVHQLDDFL

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_1084 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000000497	1 retrocopy	retro_opri_1084 ,