RetrogeneDB ID: retro_ptro_2237

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:23924420..23924980(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSPTRG00000009194
• Aliases: None
• Description: Pan troglodytes RAB5C, member RAS oncogene family (RAB5C), mRNA. [Source:RefSeq mRNA;Acc:NM_001246383]

Sequence

>retro_ptro_2237
TCTGCAGTGGGCAAATCTAACCTGTCCTCTGCCTTGTGAAGGGACAATTTCATGCATACTAGGAGAGCACACTCAGAGCA
GCCTTCCTCCCACAGAATGTCTGCTTGGACAACACAACAGTTAGGTTTGAGATCTGGGACACGGTTGGACAGCAGTGGTA
TCACAGCCTGGCCCCCATGTACTCTTGGGGGGGCCCAGGCTGCCATCATGGTCTATGACATCACCAAAACAGATACATTT
GCCGGAGCCAAGGACTGAGTGAAGGAGCTACCAAGCAGGCCAGCCCCAACATGGTCCTTGCGCTCACGGGTAACAAGGCA
GACCTGGCCAGCAAGAGACCCCTGGAATTCCAGGAAGCACAAGCCTATGCAGACGACGACAGTTGGCTGTTCATGGAGAC
ATCAGCAAAGGGTGCAATGAATGTGAATGAAATTTTCATGGCAATAGCTGAGAAACTTCCCAAGAACAAGCCCCAGAATG
CAGCTGGTGCTCCAGACAGAAACCAAGGTGTGGACCTTCAGGAGAACCACCCGGCCAGCCCCAACCAGTGTTGCAGCAAT

Alignment

ORF - retro_ptro_2237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAVGKSSL-VLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMY-YRGAQAA
          SAVGKS.L.VL..VKGQFH.Y.EST..AAFL.Q.VCLD.TTV.FEIWDT.GQ..YHSLAPMY...GAQAA
Retrocopy SAVGKSNL<VLCLVKGQFHAY*ESTLRAAFLPQNVCLDNTTVRFEIWDTVGQQWYHSLAPMY>LGGAQAA

Parental  IVVYDITNTDTFARAKNWVKEL-QRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAK
          I.VYDIT.TDTFA.AK..VKEL...QASPN.V.AL.GNKADLASKR..EFQEAQAYADD.S.LFMETSAK
Retrocopy IMVYDITKTDTFAGAKD*VKEL<TKQASPNMVLALTGNKADLASKRPLEFQEAQAYADDDSWLFMETSAK

Parental  TAMNVNEIFMAIAKKLPKNEPQNATGAPGRNRGVDLQENNPASRSQCCSN
          .AMNVNEIFMAIA.KLPKN.PQNA.GAP.RN.GVDLQEN.PAS..QCCSN
Retrocopy GAMNVNEIFMAIAEKLPKNKPQNAAGAPDRNQGVDLQENHPASPNQCCSN

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	70.03 RPM
SRP007412_cerebellum	0.07 RPM	87.97 RPM
SRP007412_heart	0.06 RPM	25.27 RPM
SRP007412_kidney	0.00 RPM	168.23 RPM
SRP007412_liver	0.00 RPM	114.70 RPM
SRP007412_testis	0.11 RPM	31.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2237 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2237 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3216
Pongo abelii	retro_pabe_2664
Macaca mulatta	retro_mmul_2022

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237 ,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,