RetrogeneDB ID: retro_ptro_2489

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:138897170..138897637(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTF3L4
• Ensembl ID: ENSPTRG00000000735
• Aliases: None
• Description: Pan troglodytes basic transcription factor 3-like 4 (BTF3L4), mRNA. [Source:RefSeq mRNA;Acc:NM_001251933]

Sequence

>retro_ptro_2489
ATGAATCAAGAAAAGTTAGCCAAACTTCAGGCTCAGGTCCGGATAGGGGGCAAGGGTACACCTCACAGAAGGAAGGTGGT
ACATAGAACAGCTATAGCTAATGACAAAAAGCTTCAGAATTATCTAAAAAAAACCTGGCTGTGTATAATATAGCTGGTAT
TGAAGAGGTGAACATGATTAAAGATGATAGGACAGTTATTCATTTCAACAATCCCAAAGTCCAAGCTTCCCTTTCTGCTA
ATACCTTTGCAATTACTGGTCATGCAGAAGCCAAATCAATCACAGAAATGCTTCCTGGAATATTAAGTCAGCTTGGTGCT
GACAGCTCAACAATCCTTAAGAAGTTACCTGAACAGTCCCCATGGCAAGTCTTGGACAGTAAAGCACCAAAACCAGAAGA
CATTGATGAGGAGGATGATGTTCTAGATCCTATAGAAAAATCTGATAAGGCATCAAAGAATGAAGCT

Alignment

ORF - retro_ptro_2489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 99.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATAD-DKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHF
          MNQEKLAKLQAQVRIGGKGT..R.K.V.......D..K....S...LAV.NIAGIEEVNMIKDD.TVIHF
Retrocopy MNQEKLAKLQAQVRIGGKGTPHRRKVVHRTAIAND<QKASELSXXXLAVYNIAGIEEVNMIKDDRTVIHF

Parental  NNPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEED
          NNPKVQASLSANTFAITGHAEAK.ITEMLPGILSQLGADS.T.L.KL.EQ.P.QVLDSKAPKPEDIDEE.
Retrocopy NNPKVQASLSANTFAITGHAEAKSITEMLPGILSQLGADSSTILKKLPEQSPWQVLDSKAPKPEDIDEE-

Parental  DDVPDLVENFDEASKNEA
          DDV.D..E..D.ASKNEA
Retrocopy DDVLDPIEKSDKASKNEA

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	29.33 RPM
SRP007412_cerebellum	0.00 RPM	18.28 RPM
SRP007412_heart	0.00 RPM	14.86 RPM
SRP007412_kidney	0.00 RPM	13.60 RPM
SRP007412_liver	0.00 RPM	9.95 RPM
SRP007412_testis	0.00 RPM	22.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2489 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2489 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3669
Pongo abelii	retro_pabe_3010

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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,
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,
Pan troglodytes	ENSPTRG00000000735	3 retrocopies	retro_ptro_1459, retro_ptro_1658, retro_ptro_2489 ,
Pan troglodytes	ENSPTRG00000016979	12 retrocopies	retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
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,
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,