RetrogeneDB ID: retro_opri_1053

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6289:121938..122343(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSOPRG00000011649
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]

Sequence

>retro_opri_1053
AGAGGACGATACCATGGGCTCACGACCACCGTGCTGAAGCAGGGCTCCAGCCAGGGCCATCCGCTTCTTCGTCATGACTT
CCCTGCGCAAGCTGGTACCGAAGCGACAACCCCAACAAGCCCATGAACCCGCTCATCACTGGGGTCTTTGGGGCCATCGC
GGGAGCTGCCAGTGTCTTTGGGAACACCCCACTGGATGTGATCAAGACCCCGGATGCAGGGGCTAGAGGCACACAAGTAC
CGCAACACGTACGACTGCGGCTTGCAGATCTTGAGGAAGGAGGGACTCAAGGCGTTCTACAAGGGCACGGTCCCCCGCCT
GGGCCGCGTGTGCCTGGACGTGGCCATCGTGTTCATCATCTACGACGAGGTGGTGAAGCTGCTGAACAAGGTGTGGAAGA
CGGAC

Alignment

ORF - retro_opri_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.97 %
• Parental protein coverage: 85.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGTYQGLTATVLKQGSNQ-AIRFFVMTSLR-NWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK
          .G.Y.GLT.TVLKQGS.Q.AIRFFVMTSLR..WYR.DNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK
Retrocopy RGRYHGLTTTVLKQGSSQ>AIRFFVMTSLR>SWYRSDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIK

Parental  T-RMQGLEAHKYRNTWDCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
          T.RMQGLEAHKYRNT.DCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
Retrocopy T>RMQGLEAHKYRNTYDCGLQILRKEGLKAFYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD

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_1053 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053 ,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,