RetrogeneDB ID: retro_opri_954

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_49607:3633..3960(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL30
• Ensembl ID: ENSOPRG00000007644
• Aliases: None
• Description: ribosomal protein L30 [Source:HGNC Symbol;Acc:10333]

Sequence

>retro_opri_954
CGAAACAAAACACTGGACCTGATGAATTCCAGTCCTGAGTTTGTGATGAAGAGCAGAAAGTAGGTGCTGGCATCCAAGCA
GTCTCTGAAGACAGTCACACAAGGCAACGTGAAGTCTGTGATCCTCACCAACACCTGCCCCGATGGGAAGAAATCTGAAA
TACAATAGTACAGAATATTGGCCAAAACTGGGGCCAGTCCCTACAACGACAATGATATTGAATGAGGCACAACATATGGA
AACTACTACTGACTCTACACTAATTTTATTATTGACCCAGGTGATTCTGATCTTATTTGAAGCATGCCAGAACAGCCTGA
TGAAAGG

Alignment

ORF - retro_opri_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.96 %
• Parental protein coverage: 95.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKKSLESINSRLQLVMKSGKYVLGYKQSLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTGVHHYSG
          R.K.L...NS....VMKS.K.VL..KQSLK...QG..K.VIL.N.CP...KSEI..Y..LAKTG...Y..
Retrocopy RNKTLDLMNSSPEFVMKSRK*VLASKQSLKTVTQGNVKSVILTNTCPDGKKSEIQ*YRILAKTGASPYND

Parental  NNIELGTACGKYYRVCTLSIIDPGDSDIIRSMPEQTGEK
          N.IE.GT..G.YY...T..IIDPGDSD.I.SMPEQ..E.
Retrocopy NDIE*GTTYGNYY*LYTNFIIDPGDSDLI*SMPEQPDER

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_954 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 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Equus caballus	ENSECAG00000021705	7 retrocopies	retro_ecab_1094, retro_ecab_227, retro_ecab_406, retro_ecab_508, retro_ecab_599, retro_ecab_63, retro_ecab_945,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Gorilla gorilla	ENSGGOG00000005502	9 retrocopies	retro_ggor_1416, retro_ggor_1663, retro_ggor_178, retro_ggor_1925, retro_ggor_2661, retro_ggor_2886, retro_ggor_3073, retro_ggor_46, retro_ggor_866,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Ochotona princeps	ENSOPRG00000007644	3 retrocopies	retro_opri_1087, retro_opri_662, retro_opri_954 ,
Pongo abelii	ENSPPYG00000018774	4 retrocopies	retro_pabe_1605, retro_pabe_178, retro_pabe_2846, retro_pabe_8,
Rattus norvegicus	ENSRNOG00000005975	19 retrocopies	retro_rnor_1, retro_rnor_1038, retro_rnor_1631, retro_rnor_1812, retro_rnor_1830, retro_rnor_1876, retro_rnor_1893, retro_rnor_1946, retro_rnor_1975, retro_rnor_2211, retro_rnor_2598, retro_rnor_2636, retro_rnor_2666, retro_rnor_2736, retro_rnor_739, retro_rnor_745, retro_rnor_753, retro_rnor_761, retro_rnor_940,