RetrogeneDB ID: retro_ptro_3171

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:137554105..137554629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSPTRG00000015920
• Aliases: None
• Description: RAB28, member RAS oncogene family [Source:UniProtKB/TrEMBL;Acc:K7BAC3]

Sequence

>retro_ptro_3171
CAAACTATAGGACTGGATTTCTTTTGAGAAGGATAACATTGCCAGGAAACTTGAATGTTACTCTCTAGTTTGGGATACAG
GAGGCCAGACAATAGGAAGCAAAATGTTGGACAGATCCATCTATGGAGCACAGGAAATCATCTTGGTATATGGTATTATG
AGTTATCAAAGCTTTGAGAATTTTTAGAAGATTAGTGAAGAAAGTGAGTGAAGAGTCAGAAACTCAGCCACTGGTTACCT
TAGTGGGCAATAAAATTGATTTGGAGCATAATCGAACAGTAAAACCTGAAAAACACTTACGGTTTTGCCAGGAAAATGGT
TTTAATAGCCACTTTGTTTCAGCCAAGGCAAGAGACTCTGTCTTCCTGTGTTTTCAAAAAGTTGTTGCTGAAATCCTTGG
AATCAAATTAAACAAAGCAGAAATAGAACAGTCACAGAGGGTGGTAAAGGCAGATATTGTAAACTACAACCAGGAACCTA
TGGCAAGAGCTGTTAACCCTTCTAGAAGCTCTGTGTGTGCAGTT

Alignment

ORF - retro_ptro_3171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.56 %
• Parental protein coverage: 90.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTIGLDFF-LRRITLPGNLNVTL-QIWDIGGQTIGGKMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTV
          QTIGLDFF.LRRITLPGNLNVTL...WD.GGQTIG.KMLD..IYGAQ...LVY.I....S....E.....
Retrocopy QTIGLDFF<LRRITLPGNLNVTL<LVWDTGGQTIGSKMLDRSIYGAQEIILVYGI---MSYQSFENF*KI

Parental  -VKKVSEESETQPLVALVGNKIDLEHMRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEILG
          .VKKVSEESETQPLV.LVGNKIDLEH.RT.KPEKHLRFCQENGF.SHFVSAK..DSVFLCFQKV.AEILG
Retrocopy >VKKVSEESETQPLVTLVGNKIDLEHNRTVKPEKHLRFCQENGFNSHFVSAKARDSVFLCFQKVVAEILG

Parental  IKLNKAEIEQSQRVVKADIVNYNQEPMSRTVNPPRSSMCAV
          IKLNKAEIEQSQRVVKADIVNYNQEPM.R.VNP.RSS.CAV
Retrocopy IKLNKAEIEQSQRVVKADIVNYNQEPMARAVNPSRSSVCAV

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	1.68 RPM	14.32 RPM
SRP007412_cerebellum	1.40 RPM	14.84 RPM
SRP007412_heart	0.55 RPM	11.48 RPM
SRP007412_kidney	0.68 RPM	12.97 RPM
SRP007412_liver	0.07 RPM	5.37 RPM
SRP007412_testis	0.00 RPM	62.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3171 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3171 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171 ,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,