RetrogeneDB ID: retro_opri_232

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3984:17110..17869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MORF4L2
• Ensembl ID: ENSOPRG00000012633
• Aliases: None
• Description: mortality factor 4 like 2 [Source:HGNC Symbol;Acc:16849]

Sequence

>retro_opri_232
ATACATTACAGTGGTTGGAATAAGAATCGGGCTGAATGGGTCCCAGAGAGCCAAGTGCTCACACACACGGATACCAATCT
ACAGAGACAGCGAGAACTTCCCAAAGCCAATCAGGAACAGTACGAACAGGGGAAGATCAGAGGGGGCTGCCCCAGGAAAG
ACGACACCTGGCCTACAACAGAAACTTGTGGAAGTGAAAACAAAGAGAAACAAACAGAAAATACCTACAAATGGAGGTGG
TGGTGGCACCAGGGAGACACCTCGGTTGCCTTGGAAGAAAAGGGGCCAAGTAGATCCTACTGTTGGAAGTGAAGAGACAT
TCATGAACAGAGCAGAAGTTAAAGTGAAGATTCCTGAGGAGCTAAAGCCATGGCTTGTTGATGACCAGGGACTTAATTAC
CAAACAACAGCTCTTTTTCTTCCTGCCCCCCAAAAAAAAAAAAAGTGTGTATTTCATTCGGGAGATTATGCAAATCACAA
GAAATCTCCTGGAATCAGACAATAAGGAAATGGCTGTTAATCAAGCTGTAGCAGGGGTAAGAGAGTACTTCGATGTCATG
TTGGGCACTCAGCTGCTCTACATGTTTGAGGGACCCCAGTATGCGGAGATCCTCTCCAATCACCCAGATGCACCCACATT
CCAGGTATATGGGGACACCACATCTGTTGTGATTTCTGTGAACCAGAGCAATGTTGGCCTTTGCACCTCTGGAAGATAAG
GGTCCTGCTTTCTTACTGAATTACTCTCACGATTTCCTG

Alignment

ORF - retro_opri_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 82.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VHHPLLTSSWDEWVPESRVLKYVDTNLQKQRELQKANQEQYAEGKMRG-AAPGKKTSGLQQKNVDVKTKK
          .H.........EWVPES.VL...DTNLQ.QREL.KANQEQY..GK.RG.AAPGK.T.GLQQK.V.VKTK.
Retrocopy IHYSGWNKNRAEWVPESQVLTHTDTNLQRQRELPKANQEQYEQGKIRG>AAPGKTTPGLQQKLVEVKTKR

Parental  NKQKAPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDW-DLITRQKQL
          NKQK.P.NG.GG.T.ETP..P.KKR..VDPTV..EETFMNR.EVKVKIPEELKPWLVDD..DLIT.Q...
Retrocopy NKQKIPTNGGGGGTRETPRLPWKKRGQVDPTVGSEETFMNRAEVKVKIPEELKPWLVDDQ>DLITKQQLF

Parental  FYL-PAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHP
          F.L.P......................DNKE.AVN..VAG..EYF.VMLGTQLLY.FE.PQYAEIL..HP
Retrocopy FFLPPXXXXXVYFIREIMQITRNLLESDNKEMAVNQAVAGVREYFDVMLGTQLLYMFEGPQYAEILSNHP

Parental  DAPMSQVY-GAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFL
          DAP..QVY.G.PHLL..F....AMLA..PL..K..A.LLNY.HDFL
Retrocopy DAPTFQVY>GTPHLL-*FL*TRAMLAFAPLEDKGPAFLLNYSHDFL

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_232 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Ochotona princeps	ENSOPRG00000012633	5 retrocopies	retro_opri_1048, retro_opri_1193, retro_opri_232 , retro_opri_240, retro_opri_407,