RetrogeneDB ID: retro_opri_25

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1063:30585..31077(-)
• Located in intron of: ENSOPRG00000012653

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A31
• Ensembl ID: ENSOPRG00000004154
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31 [Source:HGNC Symbol;Acc:25319]

Sequence

>retro_opri_25
CTTGGTTTTGCCCACACCCACGTAGCCACCGACGTGGGGAAAGCCAGAGCTGTAAGGGAAATCAAAGGCCTTGGCAACTG
CCTGGTTAAAAATCTATAAATCTGATGGGATTAAGGGCCTGTACCAAGGCTTGAATGTGTCTGTGCAGGGAATTATCATC
TATGAGCTGCCTACTTCAGTATCTATGACACCGCAAAAAGAATGTTTCCAGATCCCAAGAAGACTCACATCTTCACCAGC
TGGATGAGTGCCGTCTGTCACAGCTGTGGCTGGGCTGACTTCCTATCCGTTTGACCCTGTTTGGTGACGCATGATAATGC
AGTCAGGGTGCAAAGGAAATGACATCATGCACACAGGCACACTGGATTGCTGGAGGAAGATTACCAAGATGAAGGCGGCA
AAGCCTTTTTCAAGAATGTGTGGTCCAATGTCCTCAGAGGCACGGGTGGTACCTTCGTGCTGGTCTTATGCAATGACATC
GAGAAGCTCATA

Alignment

ORF - retro_opri_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.07 %
• Parental protein coverage: 51.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LDFARTRLGVDIGKGPEERQFKGLGDCIVK-IAKSDGIFGLYQGFGVSVQGIIVYR-ASYFGAYDTVKGL
          L.FA.T....D.GK....R..KGLG.C.VK.I.KSDGI.GLYQG..VSVQGII.Y..A.YF..YDT.K..
Retrocopy LGFAHTHVATDVGKARAVREIKGLGNCLVK>IYKSDGIKGLYQGLNVSVQGIIIYE<AAYFSIYDTAKRM

Parental  LPKPKETPFLISFFIAQIVTTC-SGILSYPFDTVRRRMMMQSG--ETERQYKGTLDCFVKI-YQHEGMNA
          .P.PK.T....S...A.....C..G..SYPFD.V..RM.MQSG.........GTLDC..KI.YQ.EG..A
Retrocopy FPDPKKTHIFTSWMSA-VCHSC>AGLTSYPFDPVW*RMIMQSGCKGNDIMHTGTLDCWRKI<YQDEGGKA

Parental  FFRGAFSNILRGTGGALVLVLYDKIKEFL
          FF....SN.LRGTGG..VLVL...I....
Retrocopy FFKNVWSNVLRGTGGTFVLVLCNDIEKLI

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_25 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002187	1 retrocopy	retro_meug_665,
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,