RetrogeneDB ID: retro_pabe_3707

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:136358110..136358755(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSPPYG00000014610
• Aliases: None
• Description: ras-related protein Rab-28 [Source:RefSeq peptide;Acc:NP_001124634]

Sequence

>retro_pabe_3707
ATGTAGGACTCTAAGGAAGAGAGCCAGGATCAGCACTGAAAATCATCGTGCTAGGGAACAGCACCTCCCGGAAGACCTCC
TCAGCTACAGATTTTGCCCAAAAAACTTTCAGGAACCAGTACAAACTATAGGACTGGATTTCTTCTGAGAAGGATAACAT
TGCCAGGAAACTTGAATGTTACTCTCTAGTTTGGGATATAGGAGGCCAGACAATAGGAAGGAAAATGTTGGACAGATGCA
TCTATGGAGCACAGGAAATCATCTTGGTATATGATATTACGAGTTATCAAAGCTTTGAGAATTTTTAGAAGATTAGTGAA
GAAAGTGAGTGAAGAGTCAGAAACTCAGCCACTGGTTGCCTTAATGGGCAATAAAATTGATTTGGAGCATAATCAAACAG
TAAAACCTGAAAAACACTTACGGTTTTGCCAGGAAAATGGTTTTAATAGCCACTTTGTTTCAGCCAAGGCCAGAGACTCT
GTCTTCCTGTGTTTTCAAAAAGTTGTTGCTGAAATCCTTGGAATCAAATTAAACAAAGCAGAAATAGAACAGTCACAGAG
GGTGGTAAAGGCAGATATTGTAAACTACAACCAGGAACCTATGGCAAGAGCTGTTAACCCTTCTAGAAGCTCTGTGTGTG
CAGTT

Alignment

ORF - retro_pabe_3707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.78 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSDSEEESQDRQ-LKIVVLGDGASGKTS-LATCFAQETFGKRYKQTIGLDFF-LRRITLPGNLNVTL-QI
          M.DS.EESQD...LKI.VLG...S.KTS.L...F....F.....QTIGLDFF.LRRITLPGNLNVTL...
Retrocopy M*DSKEESQDQH<LKIIVLGNSTSRKTS<LSYRFCPKNFQEPV-QTIGLDFF<LRRITLPGNLNVTL<LV

Parental  WDIGGQTIGGKMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTV-VKKVSEESETQPLVALVGNKIDLEH
          WDIGGQTIG.KMLD..IYGAQ...LVYDIT...S....E......VKKVSEESETQPLVAL.GNKIDLEH
Retrocopy WDIGGQTIGRKMLDRCIYGAQEIILVYDIT---SYQSFENF*KI>VKKVSEESETQPLVALMGNKIDLEH

Parental  MRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEIVGIKLNKAEIEQSQRVVKADIVNYNQEP
          ..T.KPEKHLRFCQENGF.SHFVSAK..DSVFLCFQKV.AEI.GIKLNKAEIEQSQRVVKADIVNYNQEP
Retrocopy NQTVKPEKHLRFCQENGFNSHFVSAKARDSVFLCFQKVVAEILGIKLNKAEIEQSQRVVKADIVNYNQEP

Parental  MSRTVNPPRSSMCAV
          M.R.VNP.RSS.CAV
Retrocopy MARAVNPSRSSVCAV

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	0.88 RPM	13.71 RPM
SRP007412_cerebellum	3.89 RPM	19.46 RPM
SRP007412_heart	1.20 RPM	6.41 RPM
SRP007412_kidney	1.13 RPM	8.35 RPM
SRP007412_liver	0.61 RPM	5.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3707 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3707 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4762
Gorilla gorilla	retro_ggor_2966

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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,