RetrogeneDB ID: retro_opri_840

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3634:52142..52487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP7
• Ensembl ID: ENSOPRG00000000992
• Aliases: None
• Description: fatty acid binding protein 7, brain [Source:HGNC Symbol;Acc:3562]

Sequence

>retro_opri_840
ATGGTGGACGCCTTCCTGGCCACCTGGAAACTAGTAGAAAGCAAGAATTTCGATGACTACATGAAGTCACTCGGTGTGGG
TTTTGCTACCAGGCAAGTGCCCAATACGACCAAGTCCACCACAATCGAGAAGAAAGGCAACGCTATTGTCCTAAAAACAC
AGAGCATCTTCAAGAACACAGACATCCGCTTCAAGCTGGGGGTGGAGTTCGATGAGACCACAGCAAATGACAGGATGGTT
AAGTCCATTGTGACACTGGATGGTGACAAGCTTGTCCATGTGCAGAAGTGGGATGGACAGGAGACGACATTAGTGCGGGA
ACTAAGTGACGGCAAACTCTTCCTG

Alignment

ORF - retro_opri_840 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.93 %
• Parental protein coverage: 78.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVEAFCATWKLVDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGDKVVIRTQSTFKNTEISFRLGQE
          MV.AF.ATWKLV.S.NFD.YMK.LGVGFATRQV.N.TK.T.I....G...V..TQS.FKNT.I.F.LG.E
Retrocopy MVDAFLATWKLVESKNFDDYMKSLGVGFATRQVPNTTKSTTI-EKKGNAIVLKTQSIFKNTDIRFKLGVE

Parental  FDELSVDDRNCKSVISLNGDKLVHVQKWDGKQTVFVREIKDGKMIV
          FDE....DR..KS...L.GDKLVHVQKWDG..T..VRE..DGK...
Retrocopy FDETTANDRMVKSIVTLDGDKLVHVQKWDGQETTLVRELSDGKLFL

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_840 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014056	1 retrocopy	retro_cpor_34,
Homo sapiens	ENSG00000164434	1 retrocopy	retro_hsap_536,
Gorilla gorilla	ENSGGOG00000025475	1 retrocopy	retro_ggor_489,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874,
Otolemur garnettii	ENSOGAG00000031110	1 retrocopy	retro_ogar_2821,
Ochotona princeps	ENSOPRG00000000992	1 retrocopy	retro_opri_840 ,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,