RetrogeneDB ID: retro_pabe_2389

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:178651200..178651660(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000014310
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EEF1B2
• Ensembl ID: ENSPPYG00000013107
• Aliases: None
• Description: eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]

Sequence

>retro_pabe_2389
GGAGTAAAGAAACCTTTGGGCAAATATGGTCCTGCTAATGTAGAAGACACTACAGGAAGCAGAGCTGCAAATAGTAAAGA
TGATGATGACACTGATCTCCTTGGATCTGATAAGGAGGAGGAAAGTGAAGCAGCAAAGAGGTTAATGGAAGAATGGCTTG
CCTATAATGAATCAAAGAAAGCCAAAAAACGTGCACTTGTTGCCGTTTTCCATCATACTAGATATGAAACCGTGGGATGA
TGTGGCAGATATGGCAAAACTAGAGGAATGTGTTAGAAGCATTCAAGCAGATGGCTTAGTCTAGGGCTCTTCTAAACTAG
TTCTGATGGGATATGGAATTTAAAAACGTCAAATCCAGTGTGTAATTGAAGATGATAAAGTTGGAACAGATATGCTGGAA
GAGCAGGTCACTGCTTTTGAGGATTCTGTGTAGTCTATGGATATGGCTGCTTTCCATAAG

Alignment

ORF - retro_pabe_2389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYES-KKAKKPALVAK
          GVKK.LGKYGPA.VEDTTGS.A..SKDDDD.DL.GSD.EEESE.AKRL.EE.LA..ES..K.K...L...
Retrocopy GVKKPLGKYGPANVEDTTGSRAANSKDDDDTDLLGSDKEEESEAAKRLMEEWLAYNES>RKPKNVHLLP-

Parental  SSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
          .SI.LD.KPWDD..DMAKLEECVRSIQADGLV.GSSKLV..GYGI.K.QIQCV.EDDKVGTDMLEEQ.TA
Retrocopy FSIILDMKPWDDVADMAKLEECVRSIQADGLV*GSSKLVLMGYGI*KRQIQCVIEDDKVGTDMLEEQVTA

Parental  FEDYVQSMDVAAFNK
          FED.V.SMD.AAF.K
Retrocopy FEDSV*SMDMAAFHK

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	68.23 RPM
SRP007412_cerebellum	0.00 RPM	64.45 RPM
SRP007412_heart	0.00 RPM	103.13 RPM
SRP007412_kidney	0.00 RPM	128.28 RPM
SRP007412_liver	0.00 RPM	234.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2389 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2389 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2883
Gorilla gorilla	retro_ggor_2000
Macaca mulatta	retro_mmul_1456

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003015	1 retrocopy	retro_amel_427,
Bos taurus	ENSBTAG00000021979	8 retrocopies	retro_btau_1127, retro_btau_1309, retro_btau_1786, retro_btau_366, retro_btau_367, retro_btau_450, retro_btau_512, retro_btau_792,
Canis familiaris	ENSCAFG00000029635	1 retrocopy	retro_cfam_56,
Choloepus hoffmanni	ENSCHOG00000013835	1 retrocopy	retro_chof_725,
Callithrix jacchus	ENSCJAG00000005805	2 retrocopies	retro_cjac_176, retro_cjac_341,
Cavia porcellus	ENSCPOG00000014496	4 retrocopies	retro_cpor_1116, retro_cpor_1381, retro_cpor_1407, retro_cpor_296,
Dipodomys ordii	ENSDORG00000003669	2 retrocopies	retro_dord_510, retro_dord_592,
Felis catus	ENSFCAG00000010239	1 retrocopy	retro_fcat_1735,
Homo sapiens	ENSG00000114942	9 retrocopies	retro_hsap_1154, retro_hsap_1500, retro_hsap_2397, retro_hsap_2883, retro_hsap_3332, retro_hsap_3480, retro_hsap_3657, retro_hsap_3903, retro_hsap_4795,
Gorilla gorilla	ENSGGOG00000007002	2 retrocopies	retro_ggor_134, retro_ggor_2000,
Macropus eugenii	ENSMEUG00000002654	8 retrocopies	retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Microcebus murinus	ENSMICG00000010607	3 retrocopies	retro_mmur_1067, retro_mmur_615, retro_mmur_78,
Myotis lucifugus	ENSMLUG00000016602	8 retrocopies	retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Macaca mulatta	ENSMMUG00000001054	6 retrocopies	retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Nomascus leucogenys	ENSNLEG00000007098	8 retrocopies	retro_nleu_1220, retro_nleu_1676, retro_nleu_2078, retro_nleu_2107, retro_nleu_2521, retro_nleu_2630, retro_nleu_624, retro_nleu_834,
Oryctolagus cuniculus	ENSOCUG00000009848	4 retrocopies	retro_ocun_1014, retro_ocun_1240, retro_ocun_544, retro_ocun_922,
Otolemur garnettii	ENSOGAG00000011229	3 retrocopies	retro_ogar_2628, retro_ogar_616, retro_ogar_862,
Oreochromis niloticus	ENSONIG00000017630	1 retrocopy	retro_onil_28,
Ochotona princeps	ENSOPRG00000017163	3 retrocopies	retro_opri_1192, retro_opri_294, retro_opri_748,
Oryzias latipes	ENSORLG00000018533	1 retrocopy	retro_olat_16,
Procavia capensis	ENSPCAG00000013348	1 retrocopy	retro_pcap_154,
Pongo abelii	ENSPPYG00000013107	7 retrocopies	retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389 , retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Pteropus vampyrus	ENSPVAG00000017334	2 retrocopies	retro_pvam_1055, retro_pvam_56,
Sorex araneus	ENSSARG00000001524	1 retrocopy	retro_sara_463,
Sarcophilus harrisii	ENSSHAG00000017853	1 retrocopy	retro_shar_208,
Sus scrofa	ENSSSCG00000016128	1 retrocopy	retro_sscr_766,
Ictidomys tridecemlineatus	ENSSTOG00000005437	3 retrocopies	retro_itri_1263, retro_itri_813, retro_itri_873,
Tupaia belangeri	ENSTBEG00000005657	13 retrocopies	retro_tbel_161, retro_tbel_2046, retro_tbel_2094, retro_tbel_2298, retro_tbel_2700, retro_tbel_2776, retro_tbel_3143, retro_tbel_3541, retro_tbel_3542, retro_tbel_4050, retro_tbel_4073, retro_tbel_4205, retro_tbel_611,
Xiphophorus maculatus	ENSXMAG00000006050	1 retrocopy	retro_xmac_21,