RetrogeneDB ID: retro_opri_1015

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_58074:4084..4555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD164
• Ensembl ID: ENSOPRG00000014063
• Aliases: None
• Description: CD164 molecule, sialomucin [Source:HGNC Symbol;Acc:1632]

Sequence

>retro_opri_1015
ACTAACACCTCGACTGTAATGCCCACCATGATAGTGCTGACATCCAGTACGCCTGCCCCATCGACCAGCACTCCAGCACT
AGAAACGTGTGCCAGCGTGGCAGCTGTGCCTCCTGTTCTAATACTGGTATTGGTGATGTTACCTGTGTTTGGTTAGAATG
CAAAGAAAAGAGCTACTGTTCACATAATTCATCAGCGGGGTGCAAAGTGGTGAACAGCACTACTACTGCTACTGCTCCAG
TGCCAACCGCTTCTACAGCTAAAACCACAACCCGGCCTGCAACTTCTACCACAGCTACTACCTCAGGTGCAACAAATACC
ACTTTTACCCTAACCTTATCACCTGGGTGGAAGTCCACCTTTGATGCAGCCAGTTTTATTGGAGGAATTGTCTTTGTGTT
GGGGTGTGCAGGTTGTAATTTTCTTTCTCTATAAATTCTGCAAATCTAAAGAACGAAATTGCCACACTTTG

Alignment

ORF - retro_opri_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 84.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPTGTPMST-IVPTSRTPAPLTTTPALESCAS-HGSCVSCANSSIDNVTCVWLVCKEKSYCSHNSSAECK
          T.T.T.M.T.IV.TS.TPAP.T.TPALE.CAS..GSC.SC.N..I..VTCVWL.CKEKSYCSHNSSA.CK
Retrocopy TNTSTVMPTMIVLTSSTPAPSTSTPALETCAS<RGSCASCSNTGIGDVTCVWLECKEKSYCSHNSSAGCK

Parental  VMNSTESCSEPTTAPVPTASTAKTTTWPVASTTATTSGAANTTFTPTLSPGRKSTFDAASFIGGIVLVL-
          V.NST.......TAPVPTASTAKTTT.P..STTATTSGA.NTTFT.TLSPG.KSTFDAASFIGGIV.VL.
Retrocopy VVNSTTTA----TAPVPTASTAKTTTRPATSTTATTSGATNTTFTLTLSPGWKSTFDAASFIGGIVFVL>

Parental  GVQAVIFFLYKFCKSKERNYHTL
          GVQ.VIFFLYKFCKSKERN.HTL
Retrocopy GVQVVIFFLYKFCKSKERNCHTL

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_1015 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000019818	1 retrocopy	retro_mmus_2149,
Ochotona princeps	ENSOPRG00000014063	3 retrocopies	retro_opri_1015 , retro_opri_1045, retro_opri_60,