RetrogeneDB ID: retro_opri_631

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_20365:18113..19013(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCYL1
• Ensembl ID: ENSOPRG00000004009
• Aliases: None
• Description: adenosylhomocysteinase-like 1 [Source:HGNC Symbol;Acc:344]

Sequence

>retro_opri_631
GTCGCGGACATCGGCTTGGCTGCATGGGGACGCAAGGCCCTGGACATTGCCGAGAACGAGATGCCAGGCCTGATGCGCAT
GCGGGAGATGTACTCGGCATCCAAGCCACTGAAGGGTGCCCGCATTGCCGGCTGCTTGCACATGACTGTGGAGACTGCTG
TCCTCATCGAGACCCTTGCTGCCCTGGGTGCTGAGGTACAGTGGTCTAGCTGCAATATCTTTTTCACCCAGGACCATGCA
GCGGCTGCCGTTGCCAAGGCTGGCATTCCAGTGTACTCCTGGAAGGGCGAAACAGACGAGGAGTGCCTGTGGTGCATTGA
GCAGACACTCTACTTTAAGGACGGGCCCCTCAACATGATCCTGGATGATGGTGGCGACCTCACCAACCTTATCCACACCA
AGTACCCCCAGCTCCTGTCAGGCATCAGAGGCATCTCTGAGGAGACCACGACTGGGGTCCACAACCTCTACAAGATGATG
GCTAATGGGGTTCTGAAGGTGCCCGCCATCAATGTCAATGACTCTGTTACCAAGAGCAAGTTTGACAACCTGTACGGCTG
CCGGGAGTCCCTCATAGATGGCATCAAACGGGCTACAGATGTGATGATCGAAGGCAAGGTGGCAGTGGTAGCAGGCTATG
GAGATGTGGGCAAAGGCTGTACCCAGGCCCTGAGGGGTTTTGGGGCCCATGTCATCATCACCGAGATCGACCCCATCAAC
GCACTGCAGGCTGCCATGGAGGGCTATGAAGTGACCACCATGGATGAAGCCTGTAAAGAGGGCAACATCTTTGTCACCAC
CACAGGCTGTGTGGACATCATCCTTGGGCGGCACTTTGAGCAGATGAAAGATGATGCCATTGTGTGTAACATCGGACACT
TCGATGTGGAGATTGATGTC

Alignment

ORF - retro_opri_631 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53. %
• Parental protein coverage: 56.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKNIKQAEFGRREIEIAEQDMSALISLRKRAQGEKPLAGAKIVGCTHITAQTAVLIETLCALGAQCRWSA
          V..I..A..GR....IAE..M..L...R......KPL.GA.I.GC.H.T..TAVLIETL.ALGA...WS.
Retrocopy VADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCLHMTVETAVLIETLAALGAEVQWSS

Parental  CNIYSTQNEVAAALAEAGVAVFAWKGESEDDFWWCIDRCVNMDGWQANMILDDGGDLTHWVYKKYPNVFK
          CNI..TQ...AAA.A.AG..V..WKGE......WCI...........NMILDDGGDLT.....KYP....
Retrocopy CNIFFTQDHAAAAVAKAGIPVYSWKGETDEECLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLS

Parental  KIRGIVEESVTGVHRLYQLSKAGKLCVPAMNVNDSVTKQKFDNLYCCRESILDGLKRTTDVMFGGKQVVV
          .IRGI.EE..TGVH.LY.....G.L.VPA.NVNDSVTK.KFDNLY.CRES..DG.KR.TDVM..GK..VV
Retrocopy GIRGISEETTTGVHNLYKMMANGVLKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIEGKVAVV

Parental  CGYGEVGKGCCAALKALGAIVYITEIDPICALQACMDGFRVVKLNEVIRQVDVVITCTGNKNVVTREHLD
          .GYG.VGKGC..AL...GA.V.ITEIDPI.ALQA.M.G..V....E.........T.TG........H..
Retrocopy AGYGDVGKGCTQALRGFGAHVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFE

Parental  RMKNSCIVCNMGHSNTEIDV
          .MK...IVCN.GH...EIDV
Retrocopy QMKDDAIVCNIGHFDVEIDV

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_631 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012519	1 retrocopy	retro_meug_2028,
Ochotona princeps	ENSOPRG00000004009	1 retrocopy	retro_opri_631 ,