RetrogeneDB ID: retro_opri_517

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_14749:9706..10391(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSOPRG00000005957
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Sequence

>retro_opri_517
GTAGCGCCCATCGAGAGGGTCAAGCTGCTGCTGCAGGTGCAGCATGCCAGCTTGCAAATCACTGCCGATAAGCAGTACAA
GGGCATCCTCGACTGCGTGGTTTGTATCCCCAAGGAGCAGGGAGTCCTGTCCTTCTGGCGCGGCAACCTGGCCAATGTCA
TCAGATACTTCCCCACCCAGGCTCTCAACTTCGCCTTCAAAGATAAATACAAGCAGATCTTTCTGGGCGGTGTGGACAAG
AGGACCCAGTTCTGGCGCTACTTTGCAGGAAATCTGGCCTCGGGTGGCGCCGCTGGAGCCACCTCCTTGTGCTTTGTGTA
TCCCCTTGATTTTGCCCGTACCCGTCTAGCTGCCGAAGTGGGGAAAGCCGGAGCTGAAAGGAATATTCAAAGGCCTCGGC
CACTGCCTGGTTAAGATCTACAGATCTGATGGGATTAAGGGCCTGTACCAAGGCTTTAATGTGTCTGTGCAGGGAATTAT
CATCTACCGAGCTGCCTACTTCGGTATCTATGACACCGCAAAAGGAATGCTTCCAGATCCCAAGAACATTCACATCTTCA
TCAGCTGGAATATCGCACAGTCCGTCACAGCAGTGGCAGGGCTGACTTCCTATCCGTTTGACACTGTTCGGAGACGCATG
ATGATGCAGTCAGGACGCAAAGGAACTGACATGATTGCTGAAGGA

Alignment

ORF - retro_opri_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.15 %
• Parental protein coverage: 76.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKY
          VAPIERVKLLLQVQHAS.QI.A.KQYKGI.DCVV.IPKEQG.LSFWRGNLANVIRYFPTQALNFAFKDKY
Retrocopy VAPIERVKLLLQVQHASLQITADKQYKGILDCVVCIPKEQGVLSFWRGNLANVIRYFPTQALNFAFKDKY

Parental  KQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGASQRE-FSGLGDCLTKI
          KQIFLGGVD...QFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAA.VGK....R..F.GLG.CL.KI
Retrocopy KQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAAEVGKAGAERN>FKGLGHCLVKI

Parental  FKSDGLKGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQSVTAVAGLVSYPFDTV
          ..SDG.KGLYQGF.VSVQGIIIYRAAYFG.YDTAKGMLPDPKN.HI..SW.IAQSVTAVAGL.SYPFDTV
Retrocopy YRSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNIHIFISWNIAQSVTAVAGLTSYPFDTV

Parental  RRRMMMQSGRKGADIMYTG
          RRRMMMQSGRKG.D....G
Retrocopy RRRMMMQSGRKGTDMIAEG

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_517 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000004154	2 retrocopies	retro_opri_1112, retro_opri_25,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517 , retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,