RetrogeneDB ID: retro_opri_407

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11015:4690..5224(-)
• 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_407
CCTGGAAACAGAAATGGCAGAAGTACCAGCTAAGCACCCCAGCTGCCTCCTAAGAAGAGGGCACGGGCTAATCCCACTGT
CGAGAGTGAGGATGCATTCAAGGATCGAATGGAAGTTAAAGTAAAGATTCCTGAAGAGTGAAAACCATGGATTGTCGAGG
ACTGGGACTTGGTAACCAGGCAGAAGCAGCTGTCTCAACTCCCTGCTAAGAAGAATGTTGATGCAATTCTGGAAGAATAT
GCCAACTGCAAGAAGTCACAGGAAAACATCGATAACAAGGAGTATGTGGTTAATGAGGTGGAGGGAGGCATTAAGGAGTA
TTTCAATATGATGTTGGGCACTCAACTGCTCTACAAGTTTGAGAGGCCCCAGTATGCCAAGATCTTGTTGGCCCACTCTG
ATGCACCAATGTCCCAGGTCTATGAGGCACCACACCCACTGAGATTGTTTGTGAGAACTGGAGCAATGCTGGCTTATAAG
CCCCTTGATTAGAAGAGCCTTGCTCTGTTGTTGGGCTACTTGCATGATTTCCTA

Alignment

ORF - retro_opri_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.97 %
• Parental protein coverage: 58.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAK
          PGN..G.STS..PQ.P.KKRAR..PTVE.E..F..R.EVKVKIPEE.KPW.V.DWDL.TRQKQL..LPAK
Retrocopy PGNRNGRSTS*APQLPPKKRARANPTVESEDAFKDRMEVKVKIPEE*KPWIVEDWDLVTRQKQLSQLPAK

Parental  KNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQV
          KNVD.ILE.YAN.KKS..N.DNKEY.VNEV..GIKEYFN.MLGTQLLYKFERPQYA.IL..H.DAPMSQV
Retrocopy KNVDAILEEYANCKKSQENIDNKEYVVNEVEGGIKEYFNMMLGTQLLYKFERPQYAKILLAHSDAPMSQV

Parental  YGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFL
          Y.APH.LRLFVR.GAMLAY.PLD.KSLALLL.YLHDFL
Retrocopy YEAPHPLRLFVRTGAMLAYKPLD*KSLALLLGYLHDFL

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_407 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 ,