RetrogeneDB ID: retro_opri_282

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_456:231993..232421(-)
• Located in intron of: ENSOPRG00000003964

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDA
• Ensembl ID: ENSOPRG00000007364
• Aliases: None
• Description: cytidine deaminase [Source:HGNC Symbol;Acc:1712]

Sequence

>retro_opri_282
ATGGCCCGGGAGCCTCAGTCCGGTGCGCTGGAGCCGGAGTACCTGCAGCGGCTGCTGCTCTGCTCCCTGGAGGCCAAGAA
GTCGGCCTACTGCCCCACAGTCGCTTCCCCGTGGGCGCCACCCTGCTCACCCGCGACGGGAGGATCTTCTCGAGGTGCAA
CGTAGAAAATGCCTGTTACACCCTGGGCAACTGTACTGAAAGGACTGCCATCCATAAGGCCATCTCCGAAGGGTGCCAGG
ATTTCAGGGCCATCGCCATTGCCAGTGACCAGCAGGATGACTTCATCTCACCATGCGGGGCCTGCAGGCAGGTCATGAGA
GAGTTTGGCACCGACTGGGACGTGTACATGACGAAACCAGATGGCACATACGTGGTCAGGACAGTCCAGGAGCTGCTGCC
TGCTTCCTTCCTGCAGAAGTTCCAGGGA

Alignment

ORF - retro_opri_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAREPRSGALEPEYLQRLLLCSLEAKKSAYCP-YSRFPVGAALLTRDGRIFSGCNVENACYTLGNCAERT
          MAREP.SGALEPEYLQRLLLCSLEAKKSAYCP..SRFPVGA.LLTRDGRIFS.CNVENACYTLGNC.ERT
Retrocopy MAREPQSGALEPEYLQRLLLCSLEAKKSAYCP<HSRFPVGATLLTRDGRIFSRCNVENACYTLGNCTERT

Parental  AIHKAISEGCQDFRAIAIASDQQDDFISPCGACRQVMREFGTDWDVYMTKPDGTYVVRTVQELLPASFGP
          AIHKAISEGCQDFRAIAIASDQQDDFISPCGACRQVMREFGTDWDVYMTKPDGTYVVRTVQELLPASF..
Retrocopy AIHKAISEGCQDFRAIAIASDQQDDFISPCGACRQVMREFGTDWDVYMTKPDGTYVVRTVQELLPASF--

Parental  EDLQKFQG
          ..LQKFQG
Retrocopy --LQKFQG

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_282 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011900	1 retrocopy	retro_dord_61,
Macropus eugenii	ENSMEUG00000016075	6 retrocopies	retro_meug_102, retro_meug_1601, retro_meug_1617, retro_meug_2041, retro_meug_527, retro_meug_603,
Ochotona princeps	ENSOPRG00000007364	2 retrocopies	retro_opri_282 , retro_opri_603,