RetrogeneDB ID: retro_pabe_596

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:61921806..61922661(-)
• Located in intron of: ENSPPYG00000002344

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP469I1935
• Ensembl ID: ENSPPYG00000014384
• Aliases: None
• Description: Eukaryotic initiation factor 4A-II [Source:UniProtKB/Swiss-Prot;Acc:Q5R4X1]

Sequence

>retro_pabe_596
GTGATTCTGGTACTTGGAGATTATATGGAAGCAACCTGTCATGCCTGCATTGGTGGAACAATGTTCAAAATGAATGCAAA
AACTGCAGGCTGAAGCACCACATATTGTTGGTACACCAGGGAGAATGTGTGATATGTTAAACAGAAGATACCTTTTTCCA
AAATGGATCAAAATGTTTGTTTTGGATGAAGCAGATGAAATGTTCAGCCAAGGGTTTAAGGATCAAATCTATGAGATTTT
CCAAAAATTAAATACAAGTATTTAGGTTGTGTTGCTTTCTGCCATGATGCCAACTGATGTGTTGGAAGTGACCAAAAAAT
TCACTAAAGATCCTATTCAAATTCTGGTGAAAAAGGAAGACTTGAACCTTGAAGGAATCAAACAGTTTTATATCAATGTT
GAGCGAGAGGAATGGAAGTTAGATATACTTTGTGACTTGTACAAGACACCATTAAACAGGCTGTTATTTTTCTCAATACA
AGGTGCAAGGTGGACTGGCTGACTGAGAAAATACATGCCAGGGACGTCACAGTTTTTGCTCTGCATGGCGACATGGACCA
GAAGGAGAGAGATACTATCATGAGGGAATTCTGATCAGGGTCAAGCCCTGTTCTGATCACTACTGACTTGTTGGCACGTG
GGACTGATGTCCAACAAGTGTCTTTGGTTATAAACTGTGATCTACCTAGCAGTCATGAAAACTGTATTCACAGAATTGAC
AGAGGGGTCAATTTGGTAGAAAAGGTGTGGCTAAAAACTTTGTTACTGAAAAAGGCAAGAGGATTCTTCATGACACTGCG
ATTTTTCTGCAATACTACAGTGAAGGAAATGCCCATAAATGTAGCTGACTGTATT

Alignment

ORF - retro_pabe_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.55 %
• Parental protein coverage: 70.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VILALGDYMGATCHACIGGT-NVRNE-MQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADE
          VIL.LGDYM.ATCHACIGGT.NV.NE.MQKLQAEAPHIV.GTPGR..DMLNRRYL.PKWIKMFVLDEADE
Retrocopy VILVLGDYMEATCHACIGGT<NVQNE<MQKLQAEAPHIV-GTPGRMCDMLNRRYLFPKWIKMFVLDEADE

Parental  MLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVERE
          M.S.GFKDQIYEIFQKLNTSI.VVLLSA.MPTDVLEVTKKF..DPI.ILVKKE.L.LEGIKQFYINVERE
Retrocopy MFSQGFKDQIYEIFQKLNTSI*VVLLSAMMPTDVLEVTKKFTKDPIQILVKKEDLNLEGIKQFYINVERE

Parental  EWKLDTLCDLYETLTITQAVIF-LNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRV
          EWKLD.LCDLY.T........F.LNTR.KVDWLTEK.HARD.TV.ALHGDMDQKERD.IMREF.SGSS.V
Retrocopy EWKLDILCDLYKT-PLNRLLFF<LNTRCKVDWLTEKIHARDVTVFALHGDMDQKERDTIMREF*SGSSPV

Parental  LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG-GRFGRKGVAINFVTEEDKRILRD-IETFYNT
          LITTDLLARG.DVQQVSLVIN.DLP...EN.IHRI.RG.G.FGRKGVA.NFVTE..KRIL.D....F.NT
Retrocopy LITTDLLARGTDVQQVSLVINCDLPSSHENCIHRIDRG<GQFGRKGVAKNFVTEKGKRILHD>LRFFCNT

Parental  TVEEMPMNVADLI
          TV.EMP.NVAD.I
Retrocopy TVKEMPINVADCI

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	0.00 RPM	698.76 RPM
SRP007412_cerebellum	0.12 RPM	674.04 RPM
SRP007412_heart	0.21 RPM	314.82 RPM
SRP007412_kidney	0.00 RPM	319.93 RPM
SRP007412_liver	0.12 RPM	212.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_596 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_596 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_593
Pan troglodytes	retro_ptro_437
Gorilla gorilla	retro_ggor_525
Macaca mulatta	retro_mmul_2450

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 56 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,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,
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,