RetrogeneDB ID: retro_opri_726

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_26393:10799..11124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHRAC1
• Ensembl ID: ENSOPRG00000008780
• Aliases: None
• Description: chromatin accessibility complex 1 [Source:HGNC Symbol;Acc:13544]

Sequence

>retro_opri_726
CGTCACAAGGACAAGGAAACGTGCCTCCTCTCGCTGCCGGTGTCCTGGGTCTGAGTCACCACGAAAAGCTCCCCCAGGGT
GCATAGCATCAACCACAAGGAGCTGGTGCTAACTGCCAAGGCAGGCCACCGGGTTCTTTGTGCAGCTGCTGGCCACCTGC
GCTCATGGTCTCCGTGGGGCCCAGGGCAAGAAGGCCCTGACCAGCGTTGACCCGGCCAGCATCACGCAGCAGTCGGACGC
CCTGCAGTTTCACACAGACGTACTGTTCACGAAGATCTCTGTCAGCAAATACCCGAGGATGTTCATGCAGAAGCATGAGG
AGGAG

Alignment

ORF - retro_opri_726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.13 %
• Parental protein coverage: 91.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEKVGEARLVSLPLSRIRVIMKSSPEVSSI-NQEALV-LTAKATELFVQHLAICSYGHGGAQDKKALTYG
          ..K..E..L.SLP.S...V..KSSP.V.SI...E....L...AT..FVQ.LA.C..G..GAQ.KKALT..
Retrocopy RHKDKETCLLSLPVSWV*VTTKSSPRVHSINHKELVL>LPRQATGFFVQLLATCAHGLRGAQGKKALTSV

Parental  DLASITQQSDALQFLTDILPKKILASKYLKMLKERREEE
          D.ASITQQSDALQF.TD.L..KI..SKY..M.....EEE
Retrocopy DPASITQQSDALQFHTDVLFTKISVSKYPRMFMQKHEEE

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_726 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005017	1 retrocopy	retro_amel_1736,
Cavia porcellus	ENSCPOG00000010427	5 retrocopies	retro_cpor_1545, retro_cpor_721, retro_cpor_722, retro_cpor_723, retro_cpor_724,
Loxodonta africana	ENSLAFG00000001188	1 retrocopy	retro_lafr_932,
Monodelphis domestica	ENSMODG00000000756	2 retrocopies	retro_mdom_1379, retro_mdom_355,
Ochotona princeps	ENSOPRG00000008780	2 retrocopies	retro_opri_636, retro_opri_726 ,
Pan troglodytes	ENSPTRG00000020621	1 retrocopy	retro_ptro_2764,
Ictidomys tridecemlineatus	ENSSTOG00000008105	1 retrocopy	retro_itri_358,