RetrogeneDB ID: retro_opri_37

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1225:15391..15627(+)
• Located in intron of: ENSOPRG00000016299

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSOPRG00000003408
• Aliases: None
• Description: SFT2 domain containing 1 [Source:HGNC Symbol;Acc:21102]

Sequence

>retro_opri_37
AACACCTGCTTTCTAATGGGACCCATGAAGCAACTGAAGAAAATGTCTGAAATAACAAGATTGCTTGCCAGCATTATTAT
GTTTCTGCGTTTCTTCTGTATGTTGTGTGCCATCTTTTGGTGGCACAAGAAGGGGTTAGCCTTATTATTTTGCATATTGT
AGTTCTTGCCCATGACCTGTCATATATCCCTTATGCAAGGGACATGGTGATGAAGTGCTATTCTTCCCTTCTGAGC

Alignment

ORF - retro_opri_37 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.86 %
• Parental protein coverage: 51.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STCFLMGPVKQLKKMFEPTRLLATVVMLLCLFCTLCAVFWWHKK-GLALLFCILQFLSMTWYSLSYIPYA
          .TCFLMGP.KQLKKM.E.TRLLA...M.L..FC.LCA.FWWHKK.G..L.......L......LSYIPYA
Retrocopy NTCFLMGPMKQLKKMSEITRLLASIIMFLRFFCMLCAIFWWHKK<GVSLIILHIVVLA---HDLSYIPYA

Parental  RDAVMKCCSSLLS
          RD.VMKC.SSLLS
Retrocopy RDMVMKCYSSLLS

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_37 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 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37 , retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,