RetrogeneDB ID: retro_pabe_894

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:4757791..4758285(-)
• Located in intron of: ENSPPYG00000004170

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSPPYG00000014074
• Aliases: None
• Description: RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783]

Sequence

>retro_pabe_894
TCTACAGATTCGGCTGATTTTCTAACCCAAACTGTGTGTCTTGATGACACTACAGTATAGTTTGAAATATGGGATACAGC
TGGTCAAGAATGATACCGTAGCCTAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGTTGTATATGATATCACAA
ATGAGGAGTCCTTTGCAAGAGCAACAAATTGAGTTAAAGAACTTCAGAGGCAAGCGTGTCCTGGCATTGTAGTAGCTTTA
TCAGGAAACAAGGCTGACCTAGCAAATAAAAAAGCAGTAGACTTCCAGAAGCACAGTCCTATGCAGATGACAATAGTTTA
TCATTCATGAAGACATCAGCTAAAACATCAGTGAATGTAAATGAAATGTTCATGGCAATAGCTAAAAAATTGCCAAAGAA
CGAACCGCAAAATCCAGAAGCAGATTCTGCCAGAAGAAGAGGAGTAGCCCTTACTGAACCCACACAACCAAACAGGAGTC
AGTGTTGTAGTAAC

Alignment

ORF - retro_pabe_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 76.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQR
          ST..A.FLTQTVCLDDTTV.FEIWDTAGQE.Y.SLAPMYYRGAQAAIVVYDITNEESFARA.N.VKELQR
Retrocopy STDSADFLTQTVCLDDTTV*FEIWDTAGQE*YRSLAPMYYRGAQAAIVVYDITNEESFARATN*VKELQR

Parental  QASPNIVIALSGNKADLANKRAVDFQ-EAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNP
          QA.P.IV.ALSGNKADLANK.AVDFQ.EAQSYADDNSL.FM.TSAKTS.NVNE.FMAIAKKLPKNEPQNP
Retrocopy QACPGIVVALSGNKADLANKKAVDFQ<EAQSYADDNSLSFMKTSAKTSVNVNEMFMAIAKKLPKNEPQNP

Parental  GANSARGRGVDLTEPTQPTRSQCCSN
          .A.SAR.RGV.LTEPTQP.RSQCCSN
Retrocopy EADSARRRGVALTEPTQPNRSQCCSN

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	22.45 RPM
SRP007412_cerebellum	0.00 RPM	25.54 RPM
SRP007412_heart	0.00 RPM	12.52 RPM
SRP007412_kidney	0.00 RPM	14.15 RPM
SRP007412_liver	0.00 RPM	17.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_894 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_894 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1074
Gorilla gorilla	retro_ggor_848
Macaca mulatta	retro_mmul_839
Callithrix jacchus	retro_cjac_3268

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894 ,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,