RetrogeneDB ID: retro_pabe_2664

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:92010674..92011233(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSPPYG00000008398
• Aliases: None
• Description: Ras-related protein Rab-5C [Source:UniProtKB/Swiss-Prot;Acc:Q5R7L7]

Sequence

>retro_pabe_2664
TCTGCAGTGGGCAAATCTAGCCTGTCCTCTGCCTTGTGAAGGGACAATTTCATGCGTACTAGGAGAGCACAATCAGAGCA
GCCTTCCTCATACAGAATGTCTGCTTGGACAACACAACAGTTAGGTTTGAATCTGGGACACAGTTGGACAGGAATGGTAT
CACAGCCTGGCCCCCATGTACTCTTCGGGGGGCCCAGGCTGCCATCGTGGTCTATGACATCACCAATACAGATACATTTG
CCGGAGCCAAGAACTGAGTGAAGGAGCTACCGAGCAGGCCACCCCCAACATGGTCCTTGCACTCACGGGTAACAAGGCAG
ACCTGGCCAGCAAGAGACCCCTGGAATTCCAGGAAGCACAAGCCTATGCAGACGACGACAGTTGGCTGTTCATGGAGACA
TCAGCAAAGGCTGCAATGAATGTGAATGAAATTTTCATGTCAATAGCTGAGAAACTTCCCAAAAACAAGCCCCAGAATGC
AGCTGGTGCTCCGGACAGAAACCAAGGTGTGGATCTCCAGGAGAACCACCTGGCCAGCCCCAACCAGTGTTGCAGCAAT

Alignment

ORF - retro_pabe_2664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.58 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SAVGKSSL-VLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFE-IWDTAGQERYHSLAPMY-YRGAQA
          SAVGKSSL.VL..VKGQFH.Y.ESTI.AAFL.Q.VCLD.TTV.FE.IWDT.GQE.YHSLAPMY..RGAQA
Retrocopy SAVGKSSL<VLCLVKGQFHAY*ESTIRAAFLIQNVCLDNTTVRFE<IWDTVGQEWYHSLAPMY>LRGAQA

Parental  AIVVYDITNTDTFARAKNWVKEL-QRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSA
          AIVVYDITNTDTFA.AKN.VKEL...QA.PN.V.AL.GNKADLASKR..EFQEAQAYADD.S.LFMETSA
Retrocopy AIVVYDITNTDTFAGAKN*VKEL<TEQATPNMVLALTGNKADLASKRPLEFQEAQAYADDDSWLFMETSA

Parental  KTAMNVNEIFMAIAKKLPKNEPQNATGAPGRNRGVDLQENNPASRSQCCSN
          K.AMNVNEIFM.IA.KLPKN.PQNA.GAP.RN.GVDLQEN..AS..QCCSN
Retrocopy KAAMNVNEIFMSIAEKLPKNKPQNAAGAPDRNQGVDLQENHLASPNQCCSN

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	81.55 RPM
SRP007412_cerebellum	0.12 RPM	36.72 RPM
SRP007412_heart	0.03 RPM	18.51 RPM
SRP007412_kidney	0.03 RPM	137.82 RPM
SRP007412_liver	0.09 RPM	52.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2664 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2664 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3216
Pan troglodytes	retro_ptro_2237
Macaca mulatta	retro_mmul_2022

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
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,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664 ,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,