RetrogeneDB ID: retro_opri_1068

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6495:9151..9447(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA2
• Ensembl ID: ENSOPRG00000011684
• Aliases: None
• Description: iron-sulfur cluster assembly 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19857]

Sequence

>retro_opri_1068
CTTCTCGCGGCCTCTCCAGGACTTGAGGTGCATCCAGTGGCCTCGTTCTCCGGTGTCGAGGCTGGCAAGGGGCAGATCCA
CCTCATTGACAGCTGTGTCCATAGGCTTCCGAAGATCACCCAAAGGTCAGACTTCCTCTGATTGGAGGAGGAGGTGGGGT
GGAGGCTCCGGATTCCAATACAAGTTTTCACTGGACACGATAATCAACCCCAACGACAGAGTGTTTGAACAGGCGGAGCC
AGAGAAGTGGTGGAATCGAGAGCTTGACCTTGGTGAAAGGCGCCCGGGTGGACTTC

Alignment

ORF - retro_opri_1068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.51 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLAASPGLEARRVASSSGAEAGEGQIHLTDSCVQRLLEITEGSEFLRLEVE-GGGCSGFQYKFSLDTVIN
          LLAASPGLE...VAS.SG.EAG.GQIHL.DSCV.RL..IT..S.FL.LE.E..GG.SGFQYKFSLDT.IN
Retrocopy LLAASPGLEVHPVASFSGVEAGKGQIHLIDSCVHRLPKITQRSDFL*LEEE>WGGGSGFQYKFSLDTIIN

Parental  PDDRVFEQ-GGARVVVDS-ESLTFVKGAQVDF
          P.DRVFEQ.GGAR.VV.S.ESLT.VKGA.VDF
Retrocopy PNDRVFEQ<GGAREVVES<ESLTLVKGARVDF

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_1068 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068 , retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009,