RetrogeneDB ID: retro_opri_1048

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6201:32617..33095(-)
• 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_1048
AGGGCACGGGCTGATCCCACTGTCGAGAGCGAGGATGCATTCAAGAATCGAATGGAAGTTAAAGTGAAGATTCCTGAAGA
GTTAAAACCATGGCTTGTTGAGGACTGGGACTTGGTAACCAGGCAGAAGCAGCTGTTTCAACTCCCTGCTAAGAAGAATG
TTGATGCTATCCTGGAAGAATATGCCAACTGCAAGAAGTCACATGTACAACATCGATAACAAGGAGTACGCGGTTAATGA
GGTGGTGGGAGGGATTAAGGAGTATTTCAATGTGATGTTGGGCACTCAGCTGCTGTACAAGTTTGAGAGGCCCCAGTATG
CTGAGATTCTGTTGGCCCACCCTGATGCACCAATGTCCCAGGTCTATGGGGCACCACACCTACTGAGATTATTTGTGAGA
ATTGGAGCAATGCTGGCTTATACACCGCTTGATGAGAAGAGCCTTGCTCTGTTGTTGGGCTATTTGCATGATTTCCTA

Alignment

ORF - retro_opri_1048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRG-
          RAR.DPTVE.E..F.NR.EVKVKIPEELKPWLV.DWDL.TRQKQLF.LPAKKNVD.ILE.YAN.KKS...
Retrocopy RARADPTVESEDAFKNRMEVKVKIPEELKPWLVEDWDLVTRQKQLFQLPAKKNVDAILEEYANCKKSHV>

Parental  NTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLA
          N.DNKEYAVNEVV.GIKEYFNVMLGTQLLYKFERPQYAEIL..HPDAPMSQVYGAPHLLRLFVRIGAMLA
Retrocopy NIDNKEYAVNEVVGGIKEYFNVMLGTQLLYKFERPQYAEILLAHPDAPMSQVYGAPHLLRLFVRIGAMLA

Parental  YTPLDEKSLALLLNYLHDFL
          YTPLDEKSLALLL.YLHDFL
Retrocopy YTPLDEKSLALLLGYLHDFL

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_1048 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,