RetrogeneDB ID: retro_opri_686

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_24024:11610..12017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL28
• Ensembl ID: ENSOPRG00000000463
• Aliases: None
• Description: ribosomal protein L28 [Source:HGNC Symbol;Acc:10330]

Sequence

>retro_opri_686
ATGTCCGCGCACCTGCAGTGAATGGTCGTGCGCAACTGCTCCAGCTTCCTCATCAAGAGGAACAGCAGACGTACAACACG
GAGCCCAATAACCTCAAGACACGGAACTCGTTCCTCTACAACGGGCTGATCCACCACAAGACCGTGGGCGTGGAACCGGC
TGCGGACGGCAAGGGCGTCACGGTGGTCATGAAGCGCCAGAGCGGCCAGCAGAAGCTGGCCACCTCGTACGTGCGGACCA
CCATCAACAAGAATGCGCGGGCCACGCTCAGCAGCATTTGGCACATGATTCGCAAAAACAAGTACCGCCCCGATCTGCGC
ATGGCTGCCATCCGCAGAGCCAGCGCCAGCCTACGCAGCCAGAAGCCGGTGATGGTGAAGAGGAAGCCTACGCGTCCCAC
CAAGAGC

Alignment

ORF - retro_opri_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.78 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAHLQWMVVRNCSSFLIKRN-KQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVMKRQSG
          MSAHLQ.MVVRNCSSFLIKRN..QTY.TEPNNLK.RNSF.YNGLIH.KTVGVEPAADGKGV.VVMKRQSG
Retrocopy MSAHLQ*MVVRNCSSFLIKRN<QQTYNTEPNNLKTRNSFLYNGLIHHKTVGVEPAADGKGVTVVMKRQSG

Parental  QRKPATSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQKPVMVKRKRSRPTKS
          Q.K.ATSYVRTTINKNARATLSSI.HMIRKNKYRPDLRMAAIRRASA.LRSQKPVMVKRK..RPTKS
Retrocopy QQKLATSYVRTTINKNARATLSSIWHMIRKNKYRPDLRMAAIRRASASLRSQKPVMVKRKPTRPTKS

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_686 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 17 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015980	1 retrocopy	retro_acar_10,
Ailuropoda melanoleuca	ENSAMEG00000003764	15 retrocopies	retro_amel_1006, retro_amel_1099, retro_amel_1155, retro_amel_1369, retro_amel_1393, retro_amel_1465, retro_amel_1737, retro_amel_231, retro_amel_289, retro_amel_33, retro_amel_474, retro_amel_556, retro_amel_630, retro_amel_822, retro_amel_829,
Bos taurus	ENSBTAG00000023343	5 retrocopies	retro_btau_263, retro_btau_433, retro_btau_434, retro_btau_565, retro_btau_891,
Canis familiaris	ENSCAFG00000002585	8 retrocopies	retro_cfam_1009, retro_cfam_1192, retro_cfam_2145, retro_cfam_350, retro_cfam_462, retro_cfam_533, retro_cfam_581, retro_cfam_879,
Callithrix jacchus	ENSCJAG00000000869	1 retrocopy	retro_cjac_218,
Cavia porcellus	ENSCPOG00000012833	2 retrocopies	retro_cpor_127, retro_cpor_214,
Felis catus	ENSFCAG00000005639	15 retrocopies	retro_fcat_1045, retro_fcat_1214, retro_fcat_1397, retro_fcat_1404, retro_fcat_1463, retro_fcat_1629, retro_fcat_1663, retro_fcat_171, retro_fcat_233, retro_fcat_484, retro_fcat_575, retro_fcat_786, retro_fcat_904, retro_fcat_910, retro_fcat_942,
Loxodonta africana	ENSLAFG00000022257	2 retrocopies	retro_lafr_325, retro_lafr_548,
Macropus eugenii	ENSMEUG00000015744	1 retrocopy	retro_meug_1497,
Myotis lucifugus	ENSMLUG00000023789	1 retrocopy	retro_mluc_325,
Macaca mulatta	ENSMMUG00000015901	1 retrocopy	retro_mmul_68,
Monodelphis domestica	ENSMODG00000000275	1 retrocopy	retro_mdom_1458,
Mus musculus	ENSMUSG00000030432	10 retrocopies	retro_mmus_162, retro_mmus_1679, retro_mmus_1911, retro_mmus_2511, retro_mmus_2526, retro_mmus_2606, retro_mmus_2629, retro_mmus_3149, retro_mmus_362, retro_mmus_738,
Ochotona princeps	ENSOPRG00000000463	1 retrocopy	retro_opri_686 ,
Petromyzon marinus	ENSPMAG00000008617	1 retrocopy	retro_pmar_10,
Pongo abelii	ENSPPYG00000010417	4 retrocopies	retro_pabe_1691, retro_pabe_1869, retro_pabe_2383, retro_pabe_2778,
Rattus norvegicus	ENSRNOG00000017127	5 retrocopies	retro_rnor_1588, retro_rnor_2117, retro_rnor_243, retro_rnor_610, retro_rnor_855,