RetrogeneDB ID: retro_opri_118

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2422:21590..22979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSOPRG00000015434
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_opri_118
CACCAGCGCCTGGTGGCTAGCCTGGAGCTCCGGAAGGCCAGGAAAGATGAGCAGGCCTTGAAGAGGAGGAATATCACCAA
TTTCCCTCCTGAGCCATCTTCGGAAAAACCTGCCAAAGAGGTCAGCCTCAATCTGGATGAAATCGTGAGAGGTGTGAACA
GCTCAGACCCTGACCTTTGCTTCCAGGCCACCCTTGCAGTCAGGAAAATGCTGTCCCAGGAAAGGAACCCCCCTCTGAAG
ATGATTATTGACATGGGGCTCATCCCCAGGCTGGTGGCGTTCCTGAAGTCATCGTTGCCCTTCTTGCAGTTTGAGGCTGC
CTGGGCTCTGACCAACATCGCTTCAGGGACCTCGGAGCAGACTCGGGCCGTTGTGGAAGCAGGTGCCATCCAGCCCCTGA
TTGAGCTACTGGGCTCTACCAGTGCAGCCGTGTGTGAGCAGGCCGTGTGGGCTCTCGGCAACATAGCCGGTGATGGCCCC
GAGTTCAGAGATGCCGTCATTTCAAGCAATGCCATCCCACATCTGCTGGCCCTGGTTTGCCCAACTATAACAGTCGCATT
TCTGTGGAAATCACATGGACCTTGTCCAACCTGTGCCGGAACAAGAATCCATATCCTTGCGACGAGATGGTGAGGCAGCT
GCTGCCTGTTCTCTCTACCTCCTGCAGCACCATGACAGATAGATTGTCTCGGACACCTGCTGGGCCTTGTCCTACCTCAC
TGAGGGCTGCAACGAGCGCATTGACCGAGTGGACAACATTGGGCTCTTGCCCAGGCTGGTAGAGCTCATGACCAGTCAGG
AGCTCAGCATCCTGATTCCTCCTCTCCGCACGGTGTGCTACATTGTCACAGGAACTGAACACCAGACCCAGATGGTCATC
GACGCAGGTCTGCTGTAGGTGCTGCACCACCTCCTGAGGCACCCCAAAACCTCCATCCAGAAGGAGGCGGCCTGGGTCCT
AAGCAATGTGGCTGCAGGATCTCAACAGCAAATCCAGCTGCTGATTGTGTACGACTTTTGCTGCCTCTCTTGGTGGCTCT
GCTGAAAAATGGGGAGTTTCAAGTCCAGAAGGAGGCAGTCTGGACGGTGGCCAACTTCACAGTGGGGGCCACTGTGAGCC
AGTTGTTCCAGCTGGTCTACTCGGGGGTCTTGGAGCCCCTGGTGAATCTGCTCACCGCCCCAGATCCTAAGATTGTCCTC
ATCATCCTTGATGTCATCTCTTACTTCCTCCAGGAGGCAGAGAAGCTGCATGAGAAGGACAGACTATACTTTCTGATAGA
AGGGCTTGGCGGGATTGAAAGAATTGAGACCTTGCAGCTGCACGTGAACCAGCAGACCGCGCAGACCGCCGTGAGCCTCA
TCGAGAAGCACTTTGGCGAGGAAGAAGAC

Alignment

ORF - retro_opri_118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 94.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HQRLVASLELRKARKDEQALKRRNITNFPPEPSSEKPAKEVCVSLNLDEIVRGVNSSDPDLCFQATLAVR
          HQRLVASLELRKARKDEQALKRRNITNFPPEPSSEKPAKEV..SLNLDEIVRGVNSSDPDLCFQATLAVR
Retrocopy HQRLVASLELRKARKDEQALKRRNITNFPPEPSSEKPAKEV--SLNLDEIVRGVNSSDPDLCFQATLAVR

Parental  KMLSQERNPPLKMIIDMGLIPRLVAVPESSLPFLQFEAAWTSDNIVSGTSSQILAVVEA-AIQPLMELLD
          KMLSQERNPPLKMIIDMGLIPRLVA...SSLPFLQFEAAW...NI.SGTS.Q..AVVEA.AIQPL.ELL.
Retrocopy KMLSQERNPPLKMIIDMGLIPRLVAFLKSSLPFLQFEAAWALTNIASGTSEQTRAVVEAGAIQPLIELLG

Parental  ST-AAVCEQAR-SLCNIAGDGPEFRDAVISSNAIPHLLALVCPTITVAFLRN-ITWTLSNLCRNKNPYPC
          ST.AAVCEQA...L.NIAGDGPEFRDAVISSNAIPHLLALVCPTITVAFL...ITWTLSNLCRNKNPYPC
Retrocopy STSAAVCEQAVWALGNIAGDGPEFRDAVISSNAIPHLLALVCPTITVAFLWK<ITWTLSNLCRNKNPYPC

Parental  DEAVRQLLPVL-FHLLQHHDREIVSDTCWALSYLTEGCNERIDRVVNIGVLPRLVELMTSQELSILIPSL
          DE.VRQLLPVL...LLQHHDR.IVSDTCWALSYLTEGCNERIDRV.NIG.LPRLVELMTSQELSILIP.L
Retrocopy DEMVRQLLPVL<LYLLQHHDR*IVSDTCWALSYLTEGCNERIDRVDNIGLLPRLVELMTSQELSILIPPL

Parental  RTVGNIVTGTEHQTQMAIDAGLLKVLPHLLRHPKTSIQKEAAWVLSNVAAGS-QQQIQLLI-VYDLLPLL
          RTV..IVTGTEHQTQM.IDAGLL.VL.HLLRHPKTSIQKEAAWVLSNVAAGS.QQ...L...V..LLPLL
Retrocopy RTVCYIVTGTEHQTQMVIDAGLL*VLHHLLRHPKTSIQKEAAWVLSNVAAGSQQQIQLLIV<VRLLLPLL

Parental  VALLKNGEFQVQKEAVWTVANFTMGATVSQLFQLVYSGVLEPLVNLLTAPDPKIVLIILDVISYFLQEAE
          VALLKNGEFQVQKEAVWTVANFT.GATVSQLFQLVYSGVLEPLVNLLTAPDPKIVLIILDVISYFLQEAE
Retrocopy VALLKNGEFQVQKEAVWTVANFTVGATVSQLFQLVYSGVLEPLVNLLTAPDPKIVLIILDVISYFLQEAE

Parental  KLREKDRLYFLIEGLGGIERIETLQLHVNQQIAQTALSLIEKHFGEVSD
          KL.EKDRLYFLIEGLGGIERIETLQLHVNQQ.AQTA.SLIEKHFGE..D
Retrocopy KLHEKDRLYFLIEGLGGIERIETLQLHVNQQTAQTAVSLIEKHFGEEED

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_118 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118 ,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,