RetrogeneDB ID: retro_opri_1169

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8438:50528..51104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GM2A
• Ensembl ID: ENSOPRG00000006171
• Aliases: None
• Description: GM2 ganglioside activator [Source:HGNC Symbol;Acc:4367]

Sequence

>retro_opri_1169
ATGCGCCTTCTGATGCGGACTGCGTCCGTCATTGCTGTCACTTTGTTTCTTGTTGGTGGGGCAGTCTCCGTGGACGCCGA
CCACAGCCACCTCAGTAGCTTTTCCTGGGATAACTGTGATGATGGGAAAGATCCTGCAGTCATCAAAAGTCTAACGCTGG
AACCTGATCCCATTGTCATTCCTGGCAATGTGACCATCAGCGCTGAGGGCAAGACCAGTGAATTGCTCAGCTCTCCTCAG
AAGGTGAAATTAACTTTGGAGAAGAAAGTGGCAGGCATCTGGATCAAGATCCCCTGTGTGAAACAATTCGGCAGCTGCAC
CTATGACATCTGTCATGTGCTGGACAATTTCGTTCGCCCTGGGAAGCCCTGCCCACAGCTACTAGAAACAAATGGGATTC
CATGCCATTGTCCCATCGCAGAAGGCACCTATTCATTGCCCAGCAGCACTTTCACATTGCCTGCGCTGGTGCTGCCCAAC
TGGCTCGTCTCTGGGAACTATTACATCGAGGGCGTCCTGAGCAACGGCGAGCAGCGTTTGGCTTGTGTCAAGATCTCGGT
CTCTGTAACGGGTAAG

Alignment

ORF - retro_opri_1169 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHSQMQAALLIALGLLLIDPAVSVLHHQNHMTQPSRFSWDNCDEGKDPAVIKSLTLEPDPIVIPGNVTVS
          M...M..A..IA..L.L...AVSV.....H....S.FSWDNCD.GKDPAVIKSLTLEPDPIVIPGNVT.S
Retrocopy MRLLMRTASVIAVTLFLVGGAVSVDADHSHL---SSFSWDNCDDGKDPAVIKSLTLEPDPIVIPGNVTIS

Parental  IEGRTSVPLKSPQKVTLTVEKEVAGFWIKVPCVEQLGSCTYDDICNMLDTLIPPGQLCPEPLHTYGLPCH
          .EG.TS..L.SPQKV.LT.EK.VAG.WIK.PCV.Q.GSCTY.DIC..LD....PG..CP..L.T.G.PCH
Retrocopy AEGKTSELLSSPQKVKLTLEKKVAGIWIKIPCVKQFGSCTY-DICHVLDNFVRPGKPCPQLLETNGIPCH

Parental  CPFKEGTYSLPVSEFTVPDLEMPSWLSSGNYRIQGILSSGGEHLACVKVSASVKGK
          CP..EGTYSLP.S.FT.P.L..P.WL.SGNY.I.G.LS.G...LACVK.S.SV.GK
Retrocopy CPIAEGTYSLPSSTFTLPALVLPNWLVSGNYYIEGVLSNGEQRLACVKISVSVTGK

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_1169 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000020587	1 retrocopy	retro_ecab_510,
Homo sapiens	ENSG00000196743	2 retrocopies	retro_hsap_264, retro_hsap_2715,
Gorilla gorilla	ENSGGOG00000015302	2 retrocopies	retro_ggor_1891, retro_ggor_313,
Macropus eugenii	ENSMEUG00000010421	1 retrocopy	retro_meug_1818,
Microcebus murinus	ENSMICG00000000690	1 retrocopy	retro_mmur_518,
Myotis lucifugus	ENSMLUG00000003215	1 retrocopy	retro_mluc_920,
Macaca mulatta	ENSMMUG00000022869	1 retrocopy	retro_mmul_454,
Nomascus leucogenys	ENSNLEG00000010966	1 retrocopy	retro_nleu_866,
Oryctolagus cuniculus	ENSOCUG00000015837	1 retrocopy	retro_ocun_704,
Ochotona princeps	ENSOPRG00000006171	1 retrocopy	retro_opri_1169 ,
Pongo abelii	ENSPPYG00000015962	1 retrocopy	retro_pabe_403,
Pan troglodytes	ENSPTRG00000017431	2 retrocopies	retro_ptro_1834, retro_ptro_221,
Ictidomys tridecemlineatus	ENSSTOG00000028500	1 retrocopy	retro_itri_759,
Tursiops truncatus	ENSTTRG00000000503	1 retrocopy	retro_ttru_488,