RetrogeneDB ID: retro_opri_1031

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6009:6214..6641(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSOPRG00000016403
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_opri_1031
GCCACGCTGGCGCAGTGCGAGTTCTCCATGGGCAAAAACCCTGCTGGTGCACGGCATGAACCGCCGGGAGAGGGACAATT
ACGAAAAGATTTACCAGGACATACAGGAGAACATCGCTGGAGCGCACGAGAAAATCGTGGCGTGCAAGAAGCAGATTGTG
GAGGCCAGGCAGATCCGGAAGCACCGGCAGGAGTACGACGCCATGGCCAGGGCCATCGAGCAGCACCCGGACCGGCAGGA
CACGCTGCGGAGGCTCGAGGCCCTGGGGAGGGAGCTGGAGCAGCTCTCGCACGTCCGGGGCAGCGTGGAGGAGAAGCTGG
AGCTGAGGCGCAAGCAGTTCCACGCTCTGCTGAGTAACATCTACGAACTCCAGCAGACGCTGGAGAAGGACCAGAAGCTC
CCGGAGGTGGAGGCGCGCAGGCCGAGC

Alignment

ORF - retro_opri_1031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 72.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STLSQCEFSMGK-TLLVYDMNLREMENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALA
          .TL.QCEFSMGK.TLLV..MN.RE..NYEKIY..I...IAGAHEKI..CKKQI..A..IRK.RQEYDA.A
Retrocopy ATLAQCEFSMGK>TLLVHGMNRRERDNYEKIYQDIQENIAGAHEKIVACKKQIVEARQIRKHRQEYDAMA

Parental  KVIQHHPDRHETLRELESLGKELEHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEDA
          ..I..HPDR..TLR.LE.LG.ELE.LSH...SVE.KLELRRKQFH.LLS.I.ELQQTLE.D.KL.EVE..
Retrocopy RAIEQHPDRQDTLRRLEALGRELEQLSHVRGSVEEKLELRRKQFHALLSNIYELQQTLEKDQKLPEVEAR

Parental  QES
          ..S
Retrocopy RPS

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_1031 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031 , retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,