RetrogeneDB ID: retro_opri_945

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_48658:3030..3408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAX
• Ensembl ID: ENSOPRG00000016245
• Aliases: None
• Description: MYC associated factor X [Source:HGNC Symbol;Acc:6913]

Sequence

>retro_opri_945
CGCAGGAACGGAAACCACATCAAGGACAGCTTCCACAGCTTGCGGGACTCGGTCCGGTCCCTCCAGGGAGAGAAGGCATC
CCGGGCCCAAACCCCAGACAAAGCCACAGACTGTATCCATTCTATGTGAAGGAAAAACCACACACACCAGCAGGACATCG
ACGACCTCAAGTGGCAGAATGCTGTTCTGGAGCACCGAGTCCGTGCACTGGAGAAGACGAGGTGCCCAACTGCAGACCAA
CTACCCCTCCTCAGACAGCAGCCTTACACCAATGCCAAGGGCAGCCCCATCTCTGCCTTCGATGGAGGCTCGGACTCCAG
TTCTGAGTCGGAGCCCAAAGAGCCCCAAAGCAGGAAGAAGCTTCGAGTGGAGGCCAGC

Alignment

ORF - retro_opri_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRAL
          R....HIKDSFHSLRDSV.SLQGEKASRAQ..DKAT..I..M.RKNHTHQQDIDDLK.QNA.LE..VRAL
Retrocopy RRNGNHIKDSFHSLRDSVRSLQGEKASRAQTPDKATDCIHSM*RKNHTHQQDIDDLKWQNAVLEHRVRAL

Parental  EKARSSAQLQTNYPSSDSSLYTNAKGSTISAFDGGSDSSSESEPEEPQSRKKLRVEAN
          EK.R.....Q...P......YTNAKGS.ISAFDGGSDSSSESEP.EPQSRKKLRVEA.
Retrocopy EKTRCPTADQ--LPLLRQQPYTNAKGSPISAFDGGSDSSSESEPKEPQSRKKLRVEAS

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_945 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945 ,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,