RetrogeneDB ID: retro_ggor_525

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:85821502..85822358(+)
• Located in intron of: ENSGGOG00000015033

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A2
• Ensembl ID: ENSGGOG00000005867
• Aliases: None
• Description: None

Sequence

>retro_ggor_525
GTGATTCTGGCACTTGGAGATTATATGGGAGCAACCTGTCATGCCTGCATTGGTGGAACAAATGTTCAAAATGAATGCAA
AAACTGCAGGCTGAAGTACCACATATTGTTGCTACACCAGGGAGAATGTGTGATATGTTAAACAAAAGATACCTTTTTCC
AAAATGGATCAAAATGTTTGTTTTGGATGAAGTAGATGAAATGTTCAGCCAAGGGTTTAAGGATCAAATCTATGAGATTT
TCCAAAAATTAAATACAAGTATTTAGGTTGTGTTGCTTTCTGCCATGATGCCAACTGATGTGTTGGAAGTGACCAAAAAA
TTCACTAAAGATCCTATTCAAATTCTGGTGAAAAAGGAAGACTTGAACCTTGAAGGAATCAAACAGTTTTATATCAATGT
TGAGCAGGAGGAATGGAAGTTGGATATACTTTGTGACTTGTACAAGACACCATTAAACAGGCTGTTATTTTTCTCAATAC
AAGGTGCAAGGTGGACTGGCTGACTGAGAAAATACATGCCAGGGACGTCACAGTTTTTGCTCTGCATGGCGACATGGACC
AGAAGGAGAGAGATACTATCATGAGGGAATTCTGATCAGGGTCAAGCCCTGTTCTGATCACTATTTACTTGTTGGCACGT
GGGACTCATGTCCAACAAGTGTCTTCGGTTATAAACTATGATCTACCTAGCAGTCATGAAAACTGTATTCGCAGAATTGG
CAGAGGGGTCAATTTGGTAGAAAAGGTGTGGCTAAAAACTTTGTTACTGAGGAAGGCAAGAGGATTCTTCGTGACACTGA
GATTTTTATGCAATACTACAGTGAAGGAAATGCCCATAAATGTAGCTGACCGTATT

Alignment

ORF - retro_ggor_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VILALGDYMGATCHACIGGTNVRNE-MQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEM
          VILALGDYMGATCHACIGGTNV.NE.MQKLQAE.PHIV..TPGR..DMLN.RYL.PKWIKMFVLDE.DEM
Retrocopy VILALGDYMGATCHACIGGTNVQNE<MQKLQAEVPHIVA-TPGRMCDMLNKRYLFPKWIKMFVLDEVDEM

Parental  LSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREE
          .S.GFKDQIYEIFQKLNTSI.VVLLSA.MPTDVLEVTKKF..DPI.ILVKKE.L.LEGIKQFYINVE.EE
Retrocopy FSQGFKDQIYEIFQKLNTSI*VVLLSAMMPTDVLEVTKKFTKDPIQILVKKEDLNLEGIKQFYINVEQEE

Parental  WKLDTLCDLYETLTITQAVIF-LNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVL
          WKLD.LCDLY.T........F.LNTR.KVDWLTEK.HARD.TV.ALHGDMDQKERD.IMREF.SGSS.VL
Retrocopy WKLDILCDLYKT-PLNRLLFF<LNTRCKVDWLTEKIHARDVTVFALHGDMDQKERDTIMREF*SGSSPVL

Parental  ITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG-GRFGRKGVAINFVTEEDKRILRDIETFY-NTT
          IT..LLARG..VQQVS.VINYDLP...EN.I.RIGRG.G.FGRKGVA.NFVTEE.KRILRD.E.F..NTT
Retrocopy ITIYLLARGTHVQQVSSVINYDLPSSHENCIRRIGRG<GQFGRKGVAKNFVTEEGKRILRDTEIFM>NTT

Parental  VEEMPMNVADLI
          V.EMP.NVAD.I
Retrocopy VKEMPINVADRI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.24 RPM	643.40 RPM
SRP007412_cerebellum	0.20 RPM	467.74 RPM
SRP007412_heart	0.03 RPM	113.04 RPM
SRP007412_kidney	0.00 RPM	341.87 RPM
SRP007412_liver	0.16 RPM	228.43 RPM
SRP007412_testis	0.10 RPM	292.98 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_525 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_593
Pan troglodytes	retro_ptro_437
Pongo abelii	retro_pabe_596
Macaca mulatta	retro_mmul_2450

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 57 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,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
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,
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,