RetrogeneDB ID: retro_opri_1005

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_56319:4147..5096(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000011486
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSOPRG00000009465
• Aliases: None
• Description: suppressor of variegation 3-9 homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17287]

Sequence

>retro_opri_1005
AATGACAAGCATAATTATTTATCTCAGGTAAAGAAATGCAAAGCAATAATTCCAAAATACAATAGCAAAGCTTTGAAACC
TGCCATTGCTGAGTACATCATAAAGAAGGCCCAAACAGAGGATAGCTCTGCAGAGATGGCAAGAGGAGCTCAACAGAAGA
AAGAATCATAAAGGAATGATATTTGTTGAAAATACTGTTGACTTAGAGGGCCCACCTTCTGACTTCTACTACATCAATGA
ATACAAACCAGCTCCTGGAATCAGCCTGGTGAATGAAGCCACCTTTGGTTGTTCATGCACAGATTGCTTTTTTGAGAAAT
GCTGGCCTGCTGAAGCTGGAGTTCTTTTGGCTTATAATAAAAACCAACAAATTAAAATCCCACCTGGTACCCCCATTTAT
AAATGCAACTCGAGGTGCCAATGTGGACCTGATTGTCCCAATAGGATTGTACAAAAAGGCACACAGTATTCACTTTGCAT
CTTTCGAACTAGCAATGGCTGTGGCTGGGGTGTAAAAACACTTGTGAAGATTAAAAGAATGAGCTTCGTCATGGAATATG
TTGGAGAGGTAATCACAAGTGAAGAAGCCGAAAGACGGGGACAGTTTTATGACAACAAAGGAATTACTTATCTCTTTGAT
CTGGACTATGAATCTGATGAGTTCACAGTGGATGCAGCTCGATATGGAAATGTGTCTCATTTTGTGAATCACAGCTGTGA
CCCAAATCTTCAGGTGTTCAATGTTTTCATTGATAACCGTGATACTCGTCTTCCCCGAATAGCATTATTTTCTACAAGAA
CCATAAATGCTGGCGAAGAGTTGACTTTTGATTATCAAATGAAAGGTTTTGGAGGTGTCTCTTTAGATTCGATTGACCAT
AGCCCAGCTAAAAAGAAGGTCAGAACAATATGCAGATGTGGTGCTGTGACTTGCAGAGGTTACCTCAAC

Alignment

ORF - retro_opri_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.21 %
• Parental protein coverage: 77.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NDKHNYLSQVKKCKAIIPKYNNKALKPAIAEYIVKKA-KQRIALQRWQEELNRRKNHKGMIFVENTVDLE
          NDKHNYLSQVKKCKAIIPKYN.KALKPAIAEYI.KKA.KQRIALQRWQEELNRRKNHKGMIFVENTVDLE
Retrocopy NDKHNYLSQVKKCKAIIPKYNSKALKPAIAEYIIKKA>KQRIALQRWQEELNRRKNHKGMIFVENTVDLE

Parental  GPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFEKCCPAEAGVLLAYNKNQQIRIPPGTPIYECNSRC
          GPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFEKC.PAEAGVLLAYNKNQQI.IPPGTPIY.CNSRC
Retrocopy GPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFEKCWPAEAGVLLAYNKNQQIKIPPGTPIYKCNSRC

Parental  QCGPDCPNRIVQKGTQYSLCIFRTSNGCGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGIT
          QCGPDCPNRIVQKGTQYSLCIFRTSNGCGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGIT
Retrocopy QCGPDCPNRIVQKGTQYSLCIFRTSNGCGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGIT

Parental  YLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINAGEELTFDYQ
          YLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDN.DTRLPRIALFSTRTINAGEELTFDYQ
Retrocopy YLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNRDTRLPRIALFSTRTINAGEELTFDYQ

Parental  MKGSGDVSSDSIDHSPAKKRVRTICKCGAVTCRGYLN
          MKG.G.VS.DSIDHSPAKK.VRTIC.CGAVTCRGYLN
Retrocopy MKGFGGVSLDSIDHSPAKKKVRTICRCGAVTCRGYLN

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_1005 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004696	1 retrocopy	retro_cfam_574,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005 ,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852, retro_tbel_993,