RetrogeneDB ID: retro_ptro_731

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:4743135..4743627(-)
• Located in intron of: ENSPTRG00000004556

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSPTRG00000014682
• Aliases: None
• Description: None

Sequence

>retro_ptro_731
ACAGATTCAGCTGATTTTCTAACCCAAAATGTGTGTCTTGATGACACTACAGTATAGTTTGAAATACGGGATACAGCTGG
TCAAGAATGATACCGTAGCCTAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGCTGTATATGATACCACAAATG
AGGAGTCCTTTGCAAGAGCAAAAAATTGGGTTAAAGAACTTCAGAGGCAAGCATGTCCTGACATTGTAATAGCTTTATCA
GGAAACAAGGCTGACCTAGCAAATAAAAGAGCAGTAGATTTCCAGGAAGCACAGTCCTATGCAGATGACAATAGTTTATT
ATTCATGAAGACATCAGCTAAAACATCAGTGAATGTAAATGAAATGTTCGTGGCGATAGCTAAAAAATTGCCAAAGAATG
AACCACAAAATCCAGAAGCAAATTCTGCCAGAAAAAGAGGAGTAGCCCTTAGTGAACCCACACAACCAAACAGGAGTCAG
TGTTGTAGTAAC

Alignment

ORF - retro_ptro_731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 76.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ
          T..A.FLTQ.VCLDDTTV.FEI.DTAGQE.Y.SLAPMYYRGAQAAI.VYD.TNEESFARAKNWVKELQRQ
Retrocopy TDSADFLTQNVCLDDTTV*FEIRDTAGQE*YRSLAPMYYRGAQAAIAVYDTTNEESFARAKNWVKELQRQ

Parental  ASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGA
          A.P.IVIALSGNKADLANKRAVDFQEAQSYADDNSLLFM.TSAKTS.NVNE.F.AIAKKLPKNEPQNP.A
Retrocopy ACPDIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMKTSAKTSVNVNEMFVAIAKKLPKNEPQNPEA

Parental  NSARGRGGVDLTEPTQPTRNQCCSN
          NSAR.R.GV.L.EPTQP.R.QCCSN
Retrocopy NSARKR-GVALSEPTQPNRSQCCSN

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	20.20 RPM
SRP007412_cerebellum	0.04 RPM	26.10 RPM
SRP007412_heart	0.00 RPM	19.64 RPM
SRP007412_kidney	0.03 RPM	17.89 RPM
SRP007412_liver	0.03 RPM	18.53 RPM
SRP007412_testis	0.00 RPM	10.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_731 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_731 has 0 orthologous retrocopies within eutheria group .

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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	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
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,