RetrogeneDB ID: retro_opri_1003

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_55663:3..910(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A16
• Ensembl ID: ENSOPRG00000002758
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), member 16 [Source:HGNC Symbol;Acc:10986]

Sequence

>retro_opri_1003
CCCTTAGCGGCCCTGTTCCAGATGGCAGCAGCGGTGGCCCAGGCCACAGCTGACCTCTACTGGCTGTGCTCCTTCCTGGC
TGGAGGTATTCTGGATGCTGTGCCAAAACAACAGTTGCTCCTTTGGATAGATGAAAGTTTTATTGCAAGCTCACATTCAC
CATTACAAACATTTAGGAGTATTTTCTGCATTGTGTGCTGTTCCCCAAAAGAAAGGATATTTGGGATTATATAAAGGAAA
TTGGGCCATGATGATTTGGATCTTTCCCTATGGCGCAATCCAGTTTATGGCATTTGAGCATTATAAAACATTAATTACTA
CAAAGCTGGGAGTTTCTGATCATGTGCACTGGTTATTGGATGGATCTATGGCAGGTATGACTGCAGTTATCTGTACTTAC
CCTCTTGATATGGTAAGAATACGCCTAGCATTCCAGGTGAAAGGAGAGCACACCTATACAGGAATTATTCATGCCTTCAA
AACAATTTATGCAAAGGAAGGTGGCTTCTTTGGATTTTACAGAGGTCTCATGCCTACCAAATTAGGAATGGCTCCCTGTG
CAGGTGTTTCATTTTTTACTTTTGGTACCTTAAAGAGTATTGGACTTTCCTATGCTCCTACCCTTCTTAGCAGACCTTCA
TCAGACAATCCTAATGTGTTAGTTTTGAAAACTCACATAAACTTACTTTGTGGTGGTGTTGCTGGAACAATAGCACAGAC
AATATCCTATCCATTTGATGTAACTCGTCGACGAATGCAGCTGGGAACTGTTCTTCCAGAATTTGAAAAGTGCCTTACCA
TGGGGGAGACTATGAAGTATGTCTATGGACACCACGGAATTCGGAAAGGATTATATCGCGGTTTATCTCTTAATTACATC
CGCCGTGCTCCCTCCCAAGCAGTGGCT

Alignment

ORF - retro_opri_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.85 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAPGMTQAAGAGALTARRDLYWLRSFLAGGI-AGCCAKTTVAPLDR-VKVLLQAHNHHYKHLGVFSALCA
          P.....Q.A.A.A..A..DLYWL.SFLAGGI..GCCAKTTVAPLDR..KVLLQAH.HHYKHLGVFSALCA
Retrocopy PLAALFQMAAAVA-QATADLYWLCSFLAGGI<SGCCAKTTVAPLDR<MKVLLQAHIHHYKHLGVFSALCA

Parental  VPKKEGYLGLYKGNGAMMIRIFPYGAIQFMAFEHYKTLITTKLGVSGHVHRLLAGSMAGMTAVICTYPLD
          VP.K.GYLGLYKGN.AMMI.IFPYGAIQFMAFEHYKTLITTKLGVS.HVH.LL.GSMAGMTAVICTYPLD
Retrocopy VPQKKGYLGLYKGNWAMMIWIFPYGAIQFMAFEHYKTLITTKLGVSDHVHWLLDGSMAGMTAVICTYPLD

Parental  MVRIRLAFQVKGEHTYTGIIHAFKTIYAKEGGFFGFYRGLMPTKLGMAPCAGVSFFTFGTLKSIGLSYAP
          MVRIRLAFQVKGEHTYTGIIHAFKTIYAKEGGFFGFYRGLMPTKLGMAPCAGVSFFTFGTLKSIGLSYAP
Retrocopy MVRIRLAFQVKGEHTYTGIIHAFKTIYAKEGGFFGFYRGLMPTKLGMAPCAGVSFFTFGTLKSIGLSYAP

Parental  TLLSRPSSDNPNVLVLKTHINLLCGGVAGTIAQTISYPFDVTRRRMQLGTVLPEFEKCLTMRETMKYVYG
          TLLSRPSSDNPNVLVLKTHINLLCGGVAGTIAQTISYPFDVTRRRMQLGTVLPEFEKCLTM.ETMKYVYG
Retrocopy TLLSRPSSDNPNVLVLKTHINLLCGGVAGTIAQTISYPFDVTRRRMQLGTVLPEFEKCLTMGETMKYVYG

Parental  HHGIRKGLYRGLSLNYIRCVPSQAVA
          HHGIRKGLYRGLSLNYIR..PSQAVA
Retrocopy HHGIRKGLYRGLSLNYIRRAPSQAVA

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_1003 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013726	1 retrocopy	retro_cfam_1092,
Myotis lucifugus	ENSMLUG00000015241	2 retrocopies	retro_mluc_1399, retro_mluc_2012,
Monodelphis domestica	ENSMODG00000017305	1 retrocopy	retro_mdom_1534,
Ochotona princeps	ENSOPRG00000002758	1 retrocopy	retro_opri_1003 ,
Vicugna pacos	ENSVPAG00000011819	1 retrocopy	retro_vpac_630,