RetrogeneDB ID: retro_ptro_227

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:160885540..160885870(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1
• Ensembl ID: ENSPTRG00000009175
• Aliases: None
• Description: eukaryotic translation initiation factor 1 [Source:HGNC Symbol;Acc:3249]

Sequence

>retro_ptro_227
GCTATCCAGAACCTCCACTCTTTTGACCCCTTTGCTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCACTGAGGA
TTATATCCATATAAGAATTCAACAGAGAAATGGCAGGAAGACCCTTACTACTGTCCAAGGGATTGCTGATGATTATGATA
AAAAGAAACTAGTGAAGGCATTTAAGAATTTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAGTATGGAGAAGTAATT
CAGCCTCAGGGTGACCAATGCAATAACATATGCCAGTTCCTCGTAGAGCTTGGACTGGCTAAGGACGATCAGCTGAAGGT
TCATGGGTTT

Alignment

ORF - retro_ptro_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGT
          AIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFK..FACNGT
Retrocopy AIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFK-NFACNGT

Parental  VIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF
          VIEHPEYGEVIQ.QGDQ..NICQFLVE.GLAKDDQLKVHGF
Retrocopy VIEHPEYGEVIQPQGDQCNNICQFLVELGLAKDDQLKVHGF

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	0.07 RPM	303.31 RPM
SRP007412_cerebellum	0.00 RPM	215.56 RPM
SRP007412_heart	0.03 RPM	188.40 RPM
SRP007412_kidney	0.03 RPM	260.29 RPM
SRP007412_liver	0.00 RPM	169.33 RPM
SRP007412_testis	0.11 RPM	130.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_227 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_227 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_271
Gorilla gorilla	retro_ggor_318

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005620	9 retrocopies	retro_amel_1335, retro_amel_335, retro_amel_567, retro_amel_575, retro_amel_587, retro_amel_666, retro_amel_782, retro_amel_798, retro_amel_823,
Bos taurus	ENSBTAG00000002282	1 retrocopy	retro_btau_63,
Callithrix jacchus	ENSCJAG00000012120	6 retrocopies	retro_cjac_1237, retro_cjac_2089, retro_cjac_346, retro_cjac_3815, retro_cjac_600, retro_cjac_84,
Dasypus novemcinctus	ENSDNOG00000007856	11 retrocopies	retro_dnov_1098, retro_dnov_1110, retro_dnov_1368, retro_dnov_148, retro_dnov_1516, retro_dnov_1668, retro_dnov_1807, retro_dnov_2062, retro_dnov_2209, retro_dnov_402, retro_dnov_421,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Felis catus	ENSFCAG00000024455	2 retrocopies	retro_fcat_1555, retro_fcat_74,
Homo sapiens	ENSG00000173812	2 retrocopies	retro_hsap_1659, retro_hsap_271,
Macropus eugenii	ENSMEUG00000015360	6 retrocopies	retro_meug_1513, retro_meug_1635, retro_meug_2189, retro_meug_315, retro_meug_749, retro_meug_821,
Myotis lucifugus	ENSMLUG00000005077	3 retrocopies	retro_mluc_233, retro_mluc_305, retro_mluc_330,
Mustela putorius furo	ENSMPUG00000010883	6 retrocopies	retro_mputfur_1019, retro_mputfur_1072, retro_mputfur_1239, retro_mputfur_1299, retro_mputfur_41, retro_mputfur_752,
Nomascus leucogenys	ENSNLEG00000011013	3 retrocopies	retro_nleu_1482, retro_nleu_2005, retro_nleu_92,
Otolemur garnettii	ENSOGAG00000031577	6 retrocopies	retro_ogar_1349, retro_ogar_1701, retro_ogar_1940, retro_ogar_2645, retro_ogar_2899, retro_ogar_856,
Pongo abelii	ENSPPYG00000029667	1 retrocopy	retro_pabe_127,
Pan troglodytes	ENSPTRG00000009175	3 retrocopies	retro_ptro_1261, retro_ptro_227 , retro_ptro_2923,
Pteropus vampyrus	ENSPVAG00000010629	4 retrocopies	retro_pvam_1152, retro_pvam_471, retro_pvam_665, retro_pvam_923,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,
Ictidomys tridecemlineatus	ENSSTOG00000002719	15 retrocopies	retro_itri_1082, retro_itri_1184, retro_itri_1369, retro_itri_1398, retro_itri_1401, retro_itri_1716, retro_itri_1784, retro_itri_1846, retro_itri_220, retro_itri_285, retro_itri_526, retro_itri_606, retro_itri_688, retro_itri_702, retro_itri_977,
Tursiops truncatus	ENSTTRG00000017135	3 retrocopies	retro_ttru_1664, retro_ttru_224, retro_ttru_315,