RetrogeneDB ID: retro_pabe_1850

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:17264702..17265281(-)
• Located in intron of: ENSPPYG00000011295

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTF3L4
• Ensembl ID: ENSPPYG00000001353
• Aliases: None
• Description: Transcription factor BTF3 homolog 4 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC59]

Sequence

>retro_pabe_1850
AGGAATGAAAAGATTAAGAGGGGGCATATCGGGCAGCCATCTTGCTCTTGCCTCGTGCTGGTGTTGGAGGACCCTCCCTG
CTTCAGATTTACCAACAGCATGAATCAAGAAAAGTTAGCCAAACTTCAGGCTCAGGTCCAGATAGGGAGCAAGGGTACAG
CTCGCAGAAAGAAGGTGGTACATAGAACAGCCACAGCTGATGACAAAAAGCTTCAGAGTTCTCTAAAAAAAACTGGCTGT
GAATAATATAACTGGTATTGAAGAGGTGAACATGATTAAAGATGATGGGACAGTTATTCACTTCAACAATCCCAAGTCCA
AGCTTCCCTTTCTGCTAACACCTTTGCAATTACTGGTAATACAGAAGCCAAACCAATCACAGAAATGCTTCCTGGGATAT
TAAGTCCCACCTGGGATATTGGTGCTGACAGTTTAACAAGCCTTAGGAAGTCAGCTGAACAGTTCCCACAGCAAGTTTTG
GACAGTAAAGCACCAAAACCAGAAGACATTGATGAGGAGGATGATGATGTTCCTGATCTTGTAGAAAATTTTGATGAGGC
ATCTAAGAATGAAGCTAAC

Alignment

ORF - retro_pabe_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.69 %
• Parental protein coverage: 78.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRGRLSLSRLRQPSCSCRVLVLEDPPRFRFTNSMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDK
          R..........QPSCSC.VLVLEDPP.FRFTNSMNQEKLAKLQAQV.IG.KGTARRKK.VVHRTATADDK
Retrocopy RNEKIKRGHIGQPSCSCLVLVLEDPPCFRFTNSMNQEKLAKLQAQVQIGSKGTARRKK-VVHRTATADDK

Parental  KLQSSLKK-LAVNNIAGIEEVNMIKDDGTVIHFNNPK-VQASLSANTFAITGHAEAKPITEMLPGILS--
          KLQSS....LAVNNI.GIEEVNMIKDDGTVIHFNNPK.VQASLSANTFAITG..EAKPITEMLPGILS..
Retrocopy KLQSSXXX>LAVNNITGIEEVNMIKDDGTVIHFNNPK<VQASLSANTFAITGNTEAKPITEMLPGILSPT

Parental  -QLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEAN
          ...GADSLTSLRK.AEQFP.QVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEAN
Retrocopy WDIGADSLTSLRKSAEQFPQQVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEAN

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	12.50 RPM
SRP007412_cerebellum	0.00 RPM	17.63 RPM
SRP007412_heart	0.03 RPM	11.29 RPM
SRP007412_kidney	0.03 RPM	13.09 RPM
SRP007412_liver	0.03 RPM	20.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1850 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1850 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2514
Pan troglodytes	retro_ptro_1459
Gorilla gorilla	retro_ggor_81

---

Parental genes homology:

Parental genes homology involve 30 parental genes, and 132 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011025	1 retrocopy	retro_btau_1030,
Canis familiaris	ENSCAFG00000003782	2 retrocopies	retro_cfam_2135, retro_cfam_938,
Callithrix jacchus	ENSCJAG00000021582	4 retrocopies	retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus	ENSCPOG00000004006	1 retrocopy	retro_cpor_908,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dasypus novemcinctus	ENSDNOG00000003181	4 retrocopies	retro_dnov_1690, retro_dnov_1928, retro_dnov_2672, retro_dnov_921,
Erinaceus europaeus	ENSEEUG00000004502	3 retrocopies	retro_eeur_215, retro_eeur_447, retro_eeur_456,
Echinops telfairi	ENSETEG00000011923	11 retrocopies	retro_etel_1017, retro_etel_1167, retro_etel_1207, retro_etel_1409, retro_etel_1990, retro_etel_2113, retro_etel_2203, retro_etel_291, retro_etel_663, retro_etel_804, retro_etel_953,
Homo sapiens	ENSG00000134717	3 retrocopies	retro_hsap_2173, retro_hsap_2514, retro_hsap_3669,
Loxodonta africana	ENSLAFG00000016124	3 retrocopies	retro_lafr_206, retro_lafr_769, retro_lafr_947,
Macropus eugenii	ENSMEUG00000006135	10 retrocopies	retro_meug_1114, retro_meug_1164, retro_meug_1333, retro_meug_1395, retro_meug_1512, retro_meug_1663, retro_meug_2008, retro_meug_298, retro_meug_903, retro_meug_966,
Microcebus murinus	ENSMICG00000002807	1 retrocopy	retro_mmur_804,
Myotis lucifugus	ENSMLUG00000016884	1 retrocopy	retro_mluc_912,
Macaca mulatta	ENSMMUG00000003636	1 retrocopy	retro_mmul_59,
Monodelphis domestica	ENSMODG00000000770	2 retrocopies	retro_mdom_33, retro_mdom_992,
Mustela putorius furo	ENSMPUG00000006966	2 retrocopies	retro_mputfur_1444, retro_mputfur_924,
Mus musculus	ENSMUSG00000028568	2 retrocopies	retro_mmus_1134, retro_mmus_2743,
Nomascus leucogenys	ENSNLEG00000016041	2 retrocopies	retro_nleu_1439, retro_nleu_521,
Oryctolagus cuniculus	ENSOCUG00000001517	3 retrocopies	retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Otolemur garnettii	ENSOGAG00000030256	2 retrocopies	retro_ogar_2759, retro_ogar_570,
Ochotona princeps	ENSOPRG00000013335	2 retrocopies	retro_opri_719, retro_opri_974,
Procavia capensis	ENSPCAG00000006428	3 retrocopies	retro_pcap_129, retro_pcap_307, retro_pcap_373,
Pongo abelii	ENSPPYG00000001353	2 retrocopies	retro_pabe_1850 , retro_pabe_3010,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Pan troglodytes	ENSPTRG00000000735	3 retrocopies	retro_ptro_1459, retro_ptro_1658, retro_ptro_2489,
Rattus norvegicus	ENSRNOG00000008512	8 retrocopies	retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Sorex araneus	ENSSARG00000003173	2 retrocopies	retro_sara_680, retro_sara_690,
Ictidomys tridecemlineatus	ENSSTOG00000006129	6 retrocopies	retro_itri_1309, retro_itri_402, retro_itri_459, retro_itri_541, retro_itri_701, retro_itri_810,
Tupaia belangeri	ENSTBEG00000013307	30 retrocopies	retro_tbel_1050, retro_tbel_1052, retro_tbel_1178, retro_tbel_1595, retro_tbel_1642, retro_tbel_1785, retro_tbel_1883, retro_tbel_1924, retro_tbel_2245, retro_tbel_2290, retro_tbel_2532, retro_tbel_2979, retro_tbel_3092, retro_tbel_3100, retro_tbel_3340, retro_tbel_3469, retro_tbel_3483, retro_tbel_3520, retro_tbel_3583, retro_tbel_3598, retro_tbel_3986, retro_tbel_4045, retro_tbel_4278, retro_tbel_4283, retro_tbel_4563, retro_tbel_4623, retro_tbel_539, retro_tbel_701, retro_tbel_98, retro_tbel_991,
Tarsius syrichta	ENSTSYG00000013635	3 retrocopies	retro_tsyr_1576, retro_tsyr_1822, retro_tsyr_2045,