RetrogeneDB ID: retro_opri_416

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11328:2774..3278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1A
• Ensembl ID: ENSOPRG00000004979
• Aliases: None
• Description: anti-silencing function 1A histone chaperone [Source:HGNC Symbol;Acc:20995]

Sequence

>retro_opri_416
GACTTGGAGTGGAAAATCATCTACGTGGGTTCTGCAGAAAGTGAAGAATATGATCAAGTTTTAGACTCTGTTTTAGTGGC
CCTGTTCCTGCAGGACGGCATATGTTTGTATTTCAGGCAGATGCACCTAAGCCAGGACTCATTCCAGATGCTGATGCAGG
AGGCGTAACAGTTGTGCTAATTAGTTGTACCTATCGAGGCCAAGCATTTATTAGAGTTGGCTACTATGTAAATAATGAAT
ATACTGAGACAGAATTAAGGGAAAATCTGCCAGTAAAACCAGACTTTTCTAAGCTTCAGAGGAACATTTTGGCATCTAAT
CCCAGGGTCACAAGATTCCACATTAATTGGGAAGACAACACGGAAAAACTGGAAGATGCAGAGAGCAGTAATCCAAACCT
CCAGTCACTTCCTTCAACAGATGCATTACCTTCCGCCTCAAAGGAATGGTCCACGTCAGAAAACTCACTAAATGTCATGT
TTAGAATCCCACATGGACTGCATG

Alignment

ORF - retro_opri_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLEWKIIYVGSAESEEYDQVLDSVLV-GPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQE
          DLEWKIIYVGSAESEEYDQVLDSVLV.GPVPAGRHMFVFQADAP.PGLIPDADA.GVTVVLI.CTYRGQ.
Retrocopy DLEWKIIYVGSAESEEYDQVLDSVLV<GPVPAGRHMFVFQADAPKPGLIPDADAGGVTVVLISCTYRGQA

Parental  FIRVGYYVNNEYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSLLS
          FIRVGYYVNNEYTETELREN.PVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSL.S
Retrocopy FIRVGYYVNNEYTETELRENLPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSLPS

Parental  TDALPSASKGWSTSENSLNVM-LESHMDCM
          TDALPSASK.WSTSENSLNVM.LESHMDCM
Retrocopy TDALPSASKEWSTSENSLNVM>LESHMDCM

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_416 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013007	1 retrocopy	retro_chof_496,
Felis catus	ENSFCAG00000023561	1 retrocopy	retro_fcat_1357,
Myotis lucifugus	ENSMLUG00000013053	1 retrocopy	retro_mluc_1410,
Otolemur garnettii	ENSOGAG00000034346	1 retrocopy	retro_ogar_2054,
Ochotona princeps	ENSOPRG00000004979	1 retrocopy	retro_opri_416 ,
Tupaia belangeri	ENSTBEG00000000592	2 retrocopies	retro_tbel_2900, retro_tbel_4175,