RetrogeneDB ID: retro_opri_35

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1176:109672..110653(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35A1
• Ensembl ID: ENSOPRG00000019035
• Aliases: None
• Description: solute carrier family 35 (CMP-sialic acid transporter), member A1 [Source:HGNC Symbol;Acc:11021]

Sequence

>retro_opri_35
AATGTCAGTTTACTATTCAAGTTATACTGCTTGACAGTGACGCCTCTGGTGGCCGCAGCGTACACCATAGCTCTAGGGCA
TACAGGAACAACAAATACAGAGCGCTACTCTTCAACCGCAGCGGTGTGTAGGACAGAAGTTGTAAAGTCACTGCTAAGTG
TGGGACTTTTAGCTGAAGAAACTGGTAGTCTGGGTAGATTCAAGACATCTTTATGTGAAAATGTTTTTGGGAGTCCCAAG
CAACTGATGAAGTTAAGTGTGCCGTCACTAGTGCATGCTGTTCAGAACAACATGGCTCTCCTAGCCCTTAGCAATCTGGA
TGCAGCAGTGTGCCAGGTGACCTACCAACTGAAGACTCCCTGTACTGCTTTATGTACTGTTTTAATGTTAAATAGGACAC
TCAGTAAATTATAGTGGATTTCAGTTTTTATGCTGTGTGGCGGAGTCACACTTGTACAGTGGAAACCAGCCCAAGCTACA
AAAGTTGTGGTGGAGCAGACTCCATTACTAGGGTTTGGCGCCATAGCTGTTGCTGTTCTGTGCTCAGGATTTGCTGGAGT
GTATTTTGAAAAAGTTTTAAAGAGTTCAGACACTTCCCTTGGGGTGAGAAACATTCAAATGTATCTATCAGGGATTGCTG
AGGCATTAGTTGGTGTCTACTTGTCAGACGGAGCTGAAATTAAAGAAAAAGGATTTTTCTATGGTTACACACATTATGTC
TGGTTTGTTATCTTTCTGGCAAGTGTTGGAGGCCTTTACACCTCGGTGGTGGACAAGCACACCGACAACATCATGAAAGG
GTTTTCCATTGTGCTTTCCACCATTGCTTCAGCGATCCTGTTTGGATTACAGATAACACTTACCTTTACTTTGGGCACCC
TTCTTGTATGTGTTTCCATTTATATCTATGGACAACCCAGGCAAGACACTACATCCATCCAACAAGGAGAAACAGCTTCG
AAAGAAAAAATCATTGGTGTG

Alignment

ORF - retro_opri_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVSLLFKLYCLTVMTLVAAAYTIALRYTRTTSTERYFSTTAVCITEVVKLLLSVGLLAKETGSLGRFKTS
          NVSLLFKLYCLTV..LVAAAYTIAL..T.TT.TERY.ST.AVC.TEVVK.LLSVGLLA.ETGSLGRFKTS
Retrocopy NVSLLFKLYCLTVTPLVAAAYTIALGHTGTTNTERYSSTAAVCRTEVVKSLLSVGLLAEETGSLGRFKTS

Parental  LCENVFGSPKELMKLSVPSLVYAVQNNMAFLALSNLDAAVYQVTYQLKIPCTALCTVLMLNRTLSKLQWI
          LCENVFGSPK.LMKLSVPSLV.AVQNNMA.LALSNLDAAV.QVTYQLK.PCTALCTVLMLNRTLSKL.WI
Retrocopy LCENVFGSPKQLMKLSVPSLVHAVQNNMALLALSNLDAAVCQVTYQLKTPCTALCTVLMLNRTLSKL*WI

Parental  SVFMLCGGVTLVQWKPAQATKVVAEQNPLLGFGAIAVAGLCSGFAGVYFEKVLKSSDTSLWVRNIQMYLS
          SVFMLCGGVTLVQWKPAQATKVV.EQ.PLLGFGAIAVA.LCSGFAGVYFEKVLKSSDTSL.VRNIQMYLS
Retrocopy SVFMLCGGVTLVQWKPAQATKVVVEQTPLLGFGAIAVAVLCSGFAGVYFEKVLKSSDTSLGVRNIQMYLS

Parental  GIAVTLVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVVVKYTDNIMKGFSAAAAIVLSTIA
          GIA..LVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVV.K.TDNIMKGFS....IVLSTIA
Retrocopy GIAEALVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVVDKHTDNIMKGFS----IVLSTIA

Parental  SVILFGLQITLTFTLGALLVCVSIYIYGLPRQDTTSIQQGETASKEKIIGV
          S.ILFGLQITLTFTLG.LLVCVSIYIYG.PRQDTTSIQQGETASKEKIIGV
Retrocopy SAILFGLQITLTFTLGTLLVCVSIYIYGQPRQDTTSIQQGETASKEKIIGV

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_35 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000019035	2 retrocopies	retro_opri_35 , retro_opri_934,
Pan troglodytes	ENSPTRG00000018405	1 retrocopy	retro_ptro_1906,