RetrogeneDB ID: retro_opri_685

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_24000:3956..4846(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000003381
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_685
ATGACAGATGCCGCTGTGTCCTTTGCCAAGGACTTCTTGGCAGGTGAAGTGGCTGCGGCCATCTCCAAGACCGCCGTAGC
GCCCGTCGAGAGGGTCAAGCTGCTGCTGCAGGTGCAGCATGCCAGCAAGCAAATCACTGCCGATAAGCAGTACAAGGGCA
TCATCGACTGCGTGGTTCGTATCCCCAAGGAGCAGGGAGTCCTGTCCTTCTGGCGCGGTAACCTGGCCAATGTCATCAGA
TACTTCCCCACGCAGGCTCTCAACCTCGCCTTCAAAGATAAATACAAGCAGATCTTTCTGGGTGGTGTGGACAAGAGGAC
CTAGTTCTGGCGCTACTTTGCAGAAAGTCTGGCCTCGGCTGGCGCGCTGGAACCCCCTCCTTGTGCTTTGTGTATCCGTT
TGATTTTTCCCATACCCGTCTAGCTGCTGACGTGGGGAAAGCCGGAGCTGAAAGGGAATTCAAAGCCCTCGGCCAATGCC
TGGTTAAGATCTACAGATCTGACGGGATTAAGGGCATGTACCAAGGCTTTAATGTGTCTGTGCAGGAAATAATCATCTAC
CGAGCTGCCTACTTCGGTATCTATGACACCGCAAAAGGAATGCTTCCAGATCCCAAGAACACTCACATCTTCATCAGCTG
GATGATCGCACAGTCCGTCACAGCTGTGGCAGGGCTGACTTCCTATCTGCTTGACACTGTTCGGAGACGCATGTTGACGC
AGTCAGGACGCAAAGGTACTGACATCATGTACACAGGCACTCTGGGTTGCTGGAGGAAGATTGCCCGGGATGAAGGTGGC
AAAGCCTTTTTCAAGGGCGCGTGGTCCAATGTCCTCAGAGGCATGGGTCGTGCTTTTGTGCTTGCGTTATAGGATGAAAC
CAAGAAGTTC

Alignment

ORF - retro_opri_685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDQALSFLKDFLAGGIAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSF
          M.D.A.SF.KDFLAG..AAA.SKTAVAP.ERVKLLLQVQHASKQI.A.KQYKGIIDCVVRIPKEQG.LSF
Retrocopy MTDAAVSFAKDFLAGEVAAAISKTAVAPVERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGA-AGATSLCFVYPLDFART
          WRGNLANVIRYFPTQALN.AFKDKYKQIFLGGVD....FWRYFA..LAS.GA.AG..SLCFVYP.DF..T
Retrocopy WRGNLANVIRYFPTQALNLAFKDKYKQIFLGGVDKRT*FWRYFAESLASAGA<AGTPSLCFVYPFDFSHT

Parental  RLAADVGKGASQREFSGLGDCLTKIFKSDGLKGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVH
          RLAADVGK....REF..LG.CL.KI..SDG.KG.YQGF.VSVQ.IIIYRAAYFG.YDTAKGMLPDPKN.H
Retrocopy RLAADVGKAGAEREFKALGQCLVKIYRSDGIKGMYQGFNVSVQEIIIYRAAYFGIYDTAKGMLPDPKNTH

Parental  IIVSWMIAQSVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIAKDEGAKAFFKGAWSNVL
          I..SWMIAQSVTAVAGL.SY..DTVRRRM..QSGRKG.DIMYTGT..CWRKIA.DEG.KAFFKGAWSNVL
Retrocopy IFISWMIAQSVTAVAGLTSYLLDTVRRRMLTQSGRKGTDIMYTGTLGCWRKIARDEGGKAFFKGAWSNVL

Parental  RGMGGAFVLVLYDEIKKY
          RGMG.AFVL.L.DE.KK.
Retrocopy RGMGRAFVLAL*DETKKF

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_685 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,