RetrogeneDB ID: retro_opri_274

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_444:685225..685710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL13
• Ensembl ID: ENSOPRG00000015721
• Aliases: None
• Description: mitochondrial ribosomal protein L13 [Source:HGNC Symbol;Acc:14278]

Sequence

>retro_opri_274
CTGAGTTCCTTCAAGGCGTCCCAGCAGTGGGCCACTCTGCCCGAATGTGGTATCTCTTAGATGGGAAAATGCAGCCTCCT
GGAAAACTCACTGCCCTGGCGTCGATGAAACTCCAAGGGCTCCACAAAACCTATATGCCATCAACTGCGTGATTGGCAAT
CGTGTTGTCATAATGAACACAAGACATATTGCATATTCTAGAAACAAATGGAAGCAGAAAGTATACGCCTCACATTACTG
GTTACCCAGGTGGATTTAAACAACTTACAGCTGCTGAACTTCACCAGGAGGATCCAGCGGCAATTGTGTAAGTGGCTGTT
TATGGCATGCTGCCATAACCCTTCACAGAAGAACAGTGGTGCAATAACTACGTCTTTTCCCAGGTGAAAGTATTCCAGAA
GACATTTTAAAGAATTTAGTGGAAGAACTTCCTCAACCACGCAAAGTACGTAAGACGTCTCAATGAATATACGCAAAAGA
GGCTC

Alignment

ORF - retro_opri_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.21 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSSFSKASQQWATF-ARMWYLLDGKMQPPGKLAALASMKLQGLHKP-IYHQLSDCGDHVVIKNTRHIAFS
          .SSF.KASQQWAT..ARMWYLLDGKMQPPGKL.ALASMKLQGLHK...Y......G..VVI.NTRHIA.S
Retrocopy LSSF-KASQQWATL<ARMWYLLDGKMQPPGKLTALASMKLQGLHKT<LYAINCVIGNRVVIMNTRHIAYS

Parental  GNKWEQKVYSSH-TGYPGGFRQVTAAELHQRDPVAIVKLAIYGMLP-KNLHRRTMMQRLHLFPDDNIPED
          .NKW.QKVY.SH.TGYPGGF.Q.TAAELHQ.DP.AIV..A.YGMLP...LHRRT..Q.L.LFP...IPED
Retrocopy RNKWKQKVYASH>TGYPGGFKQLTAAELHQEDPAAIV*VAVYGMLP<ITLHRRTVVQ*LRLFPGESIPED

Parental  ILKNLVEELPQPRKVPK-RLDEYTQEEI
          ILKNLVEELPQPRKV.K.RL.EYTQ...
Retrocopy ILKNLVEELPQPRKVRK>RLNEYTQKRL

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_274 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274 , retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,