RetrogeneDB ID: retro_opri_498

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_14061:42609..43491(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A2
• Ensembl ID: ENSOPRG00000004170
• Aliases: None
• Description: eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]

Sequence

>retro_opri_498
CTTGCATTAAAGCTCCAAAAGGGAATTCTGGCACTTGGAGACTATATGGGAGCAACTTGCCATGCCTGCATTGGAGGAAC
AAACGTTAGAAATGAAATGTAAAAGTTGCAGGCTGAAGCACCACATATCGTTGTTGGTACACCAGGAAGAGTATTTGATA
TGTTAAACAGAAGATACCTTTCTCCAAAAAGGATCAAAATGTTTGTTTTGGATGAAGCAGATGAAATGCTGAGCCGGGGG
TTTAAGGATCAAATTTATGAAATTTTCCAAAAACTAAATACTAGTATTCAGGTTGTGCTGCTGTCTGCAACAATGCCAAC
TGATGTTTCAGAAGTGACCAAAAAATTCATGAGAGATCCAATTCAAATTCTGGTGAAAAAGAAGGAATTTACCCTTGAAG
GACTCAAACAGTTCTACATCAATGCTGGGTGAGCGGAATGGAAGTTGGATACACTTTGTGACTTGTATGAAACGTTGACC
ATTACGCGGGCTGTTATTTTTCTCAATACAAGGCGCAAAGTAGACTGGCTCACTGAGAAAATGCATGCCATGGACTTCAC
AGTTTCTGCTCTGCATGGTGACATGGACCAGAAGGAAAGAGATGTCATCATGAGAGAATTCAGATCAGGCTCAAGCTGTG
TTCTGATCACTACTGACTTGTTGGCGCGTGGGATTGATGTACAAGTATCTTTGGCCATAAACTATGATCTACCTACCTAT
TGTGAAAACTATATTCACAGAGTTGGCAGAGGGGGTCGATTTGGGAGGAAAGGCGTGGCTATAAACTTTGTTACTGAAGA
AGACAAGAGGATTCTTCGTGACATTGAGACTTTCTGCAATACTACAGTGGAGGAGATGCCCATGAATGTGGCTGACCTTA
TG

Alignment

ORF - retro_opri_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.85 %
• Parental protein coverage: 72.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVL
          LA...QK.ILALGDYMGATCHACIGGTNVRNEM.KLQAEAPHIVVGTPGRVFDMLNRRYLSPK.IKMFVL
Retrocopy LALKLQKGILALGDYMGATCHACIGGTNVRNEM*KLQAEAPHIVVGTPGRVFDMLNRRYLSPKRIKMFVL

Parental  DEADEMLSRGFKDQIYEI-SKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYI
          DEADEMLSRGFKDQIYEI..KLNTSIQVVLLSATMPTDV.EVTKKFMRDPI.ILVKK.E.TLEG.KQFYI
Retrocopy DEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVSEVTKKFMRDPIQILVKKKEFTLEGLKQFYI

Parental  NVEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSG
          N....EWKLDTLCDLYETLTIT.AVIFLNTRRKVDWLTEKMHA.DFTVSALHGDMDQKERDVIMREFRSG
Retrocopy NAG*AEWKLDTLCDLYETLTITRAVIFLNTRRKVDWLTEKMHAMDFTVSALHGDMDQKERDVIMREFRSG

Parental  SSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFY
          SS.VLITTDLLARGIDV.QVSL.INYDLPT..ENYIHR.GRGGRFGRKGVAINFVTEEDKRILRDIETF.
Retrocopy SSCVLITTDLLARGIDV-QVSLAINYDLPTYCENYIHRVGRGGRFGRKGVAINFVTEEDKRILRDIETFC

Parental  NTTVEEMPMNVADLI
          NTTVEEMPMNVADL.
Retrocopy NTTVEEMPMNVADLM

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_498 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 22 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Canis familiaris	ENSCAFG00000013659	1 retrocopy	retro_cfam_378,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Dasypus novemcinctus	ENSDNOG00000011502	5 retrocopies	retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi	ENSETEG00000018565	3 retrocopies	retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Gorilla gorilla	ENSGGOG00000005867	2 retrocopies	retro_ggor_525, retro_ggor_712,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000007377	1 retrocopy	retro_mmur_525,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys	ENSNLEG00000006633	1 retrocopy	retro_nleu_2589,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii	ENSOGAG00000010729	2 retrocopies	retro_ogar_2830, retro_ogar_943,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498 ,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus	ENSSTOG00000012601	1 retrocopy	retro_itri_858,
Tupaia belangeri	ENSTBEG00000002268	11 retrocopies	retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes	ENSTRUG00000005660	2 retrocopies	retro_trub_14, retro_trub_6,
Tarsius syrichta	ENSTSYG00000013050	3 retrocopies	retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,