RetrogeneDB ID: retro_opri_1133

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_77381:2..1079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSOPRG00000011984
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_opri_1133
ATGAACGTGGCAGCCAAGTACCGCATGGCCTCCCTCTATGTGGGCGACCTCCATCCAGACGTCACGGAGGACCTGCTGTT
CAAGAAGTTCAGCACGGTGGGACCCGTGCTGTCCATTCGCGTTTGCAGGGACCTGCTGACCCGTCGCTCCCTGGGCTATG
CCTACGTGAACTTCCTGCAGCTGGCTGATGCCCAGAAGGCGCTGGACACAATGAATTTCGATGTAGTGGAAGGTAGGGCC
ATCCGCCTCATGTGGTCCCAACGCGATGCCTACTTAAGGAAATCTGGAATTGGGAATGTCTTCATCAAAAACCTCGACAA
ATCCATCGATAACAAAACCCTGTATGAGTGTTTTTCAGCGTTTGGGAAGATCCTGTCTTCCAAGGTGATGAGCGACGATC
AAGGCTCCAAGGGCTACGCGTTCGTGCACTTTCAGAACCAGATGGCGGCCGACAGGGCCATCGAGGAGATGAACGGCAAG
TTCCTCAAGGACTGCAAGGTGTTTGTGGGCAGATTCAAACACCGCAGAGATAGGGAGGCTGAGCTGCGAAAGCACGCCAG
TGAGTTCACCAACGTGTACATCAAAAACTTCGGGGACGATATGGACGACGAGAGGCTGAGGGACATCTTCAGTAAATATG
GCAGGATTGTGAGTGTTAAGGTGATGACCAATCCCTATGGGAAATCCAGAGGGTTTGGCTTCGTGAGCTTTGACAGCCAC
GAGGCTGCCAAAAGGGCCGTGGAAGACATGAATGGAGAGGCCATCAACGGGCAGCCCCTCTTCGTAGGTCGGGCGCAGAA
GAAAGTAGAGCGACAGGCTGAGTTAAAACAAATGTTTGAACAATTGAAAAAGGAAAAGATTCGCGGGCGCCAGGCAGCAA
AACTCTATATTAAGAATCTTGACGGCAGCATCGACGATGAAAAGCTGCGGCAGGAGTTTGCCTGCTTTGGGTCCGTTAGC
AGAGTGAAGGTGATGCAGGAGGAAGGACTGAGCAAGGGCTTCGGCTTGGTCTGCTTCTCCTCTGCGGAGGAGGCCAGCCG
AGCCATGGCTGAGATGAACGGTCGTATCTTGGGCTCC

Alignment

ORF - retro_opri_1133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.28 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.AA..Y.MASLYVGDLH.DVTE..L..KFS..GPVLSIRVCRD..TRRSLGYAYVNF.Q.ADA..ALD
Retrocopy MNVAAK-YRMASLYVGDLHPDVTEDLLFKKFSTVGPVLSIRVCRDLLTRRSLGYAYVNFLQLADAQKALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDV..G..IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GSKGY
Retrocopy TMNFDVVEGRAIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYECFSAFGKILSSKVMSDDQGSKGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKDL
          AFVHF..Q.AAD.AIE.MNG..L.D.KVFVGRFK.R..REAEL...A.EFTNVYIKNFG...DDE.L.D.
Retrocopy AFVHFQNQMAADRAIEEMNGKFLKDCKVFVGRFKHRRDREAELRKHASEFTNVYIKNFGDDMDDERLRDI

Parental  FSQFGKTLSVKVMRDPTGKSKGFGFVSYEKHEDANKAVEEMNGKEIGGKVIFVGRAQKKVERQAELKRKF
          FS..G...SVKVM..P.GKS.GFGFVS...HE.A..AVE.MNG..I.G...FVGRAQKKVERQAELK..F
Retrocopy FSKYGRIVSVKVMTNPYGKSRGFGFVSFDSHEAAKRAVEDMNGEAINGQPLFVGRAQKKVERQAELKQMF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQLK.E.I...Q...LYIKNLD..IDDEKLR.EF..FGS....KVM.E.G.SKGFG.VCFSS.EEA..A.
Retrocopy EQLKKEKIRGRQAAKLYIKNLDGSIDDEKLRQEFACFGSVSRVKVMQEEGLSKGFGLVCFSSAEEASRAM

Parental  TEMNGRIVGS
          .EMNGRI.GS
Retrocopy AEMNGRILGS

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_1133 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 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133 ,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,