RetrogeneDB ID: retro_opri_1028

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_59782:6741..7482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSOPRG00000007594
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_opri_1028
GAATTGAAAAAGGCTTACTGGAAACTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGAAGAAAAGTTCAAACA
GATTTCTCAAGCTTAGGAAGTTCTTTCTGATGCGAAGAAAAGGGAATTGTATGACAAAGGAGGAGAGCAGGCAATTAAGG
AGGGTGGAGCAGGAGGTGGATTCGGCTCCCCCACGGACATCTTCGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGA
GAACGGAGAGGTAAAAATGTTGTACATCAACTCTCAGTAACCTTAGAAGACTTATATAATGGTGCAACGAGAAAACTGGC
TCTGCAGAAGAATGTGATTTGCGACAAATGTGAAGGCCCAGGCAGTAAGAAAGGGGTATGCTGTCCCAACTGCCCACGTA
CTGGAATGCAAATAAGAATCCGTCAGATAGGACCTGAAATGGCTCAGCAAATTTAATCTGTATGCATGGAATGTCAGGAC
CACAGAGAACTCATCAGGCCTAAAGAGAGATGTAGAAGCAGCAATGGAAGGAAAATAGTTCGAGAGAAGAAAATTCTAGA
AGTTCATATTGACAAAGGCATGAAGGATGGCCAAAAGATAACATTCCATGGTGAAGGAGACCAAGAACCAGGATTGGAGC
TAGGAAACACCATTGTGCTAGACCAGAAAGCCTGTGATGTTTTTATTTGATGAGGAGAGAATGCTTTCATGTGTAGGGAC
ATGGAATTGGTGGAAGCATTA

Alignment

ORF - retro_opri_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.72 %
• Parental protein coverage: 58.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIKKAYRKLALKYHPDKNPDEGEKFKLISQAYEVLSDPKKRDIYDQGGEQAIKEGGSGSPSFSSPMDIFD
          E.KKAY.KLALKYHPDKNP.E.EKFK.ISQA.EVLSD.KKR..YD.GGEQAIKEGG.G...F.SP.DIFD
Retrocopy ELKKAYWKLALKYHPDKNPNEEEKFKQISQA*EVLSDAKKRELYDKGGEQAIKEGGAGG-GFGSPTDIFD

Parental  MFFGGGGRMARERRGKNVVHQLSVTLEDLYNGVTKKLALQKNVICEKCEGIGGKKGSVEKCPLCKGRGMQ
          MFFGGGGRM.RERRGKNVVHQLSVTLEDLYNG.T.KLALQKNVIC.KCEG.G.KKG....CP.C...GMQ
Retrocopy MFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGPGSKKGVC--CPNCPRTGMQ

Parental  VHIQQIGPGMVQQIQTVCIECKGQGERINPKDRCEGCSGAKVVREKKIIEVHVEKGMKDGQKILFHGEGD
          ..I.QIGP.M.QQI..VC.EC....E.I.PK.RC....G.K.VREKKI.EVH..KGMKDGQKI.FHGEGD
Retrocopy IRIRQIGPEMAQQI*SVCMECQDHRELIRPKERCRSSNGRKIVREKKILEVHIDKGMKDGQKITFHGEGD

Parental  QEPELEPGDVIIVLDQKDHSVFQRRGHDLIMKMKIQLSEAL
          QEP.LE.G...IVLDQK...VF...G....M.....L.EAL
Retrocopy QEPGLELGNT-IVLDQKACDVFI**GENAFMCRDMELVEAL

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_1028 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 10 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028 ,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,