RetrogeneDB ID: retro_ptro_220

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:146743351..146743896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN5
• Ensembl ID: ENSPTRG00000007891
• Aliases: None
• Description: dynactin subunit 5 [Source:RefSeq peptide;Acc:NP_001233429]

Sequence

>retro_ptro_220
ATGGAGTTAGGTGAGCTGCTCTACAACAAGTCTGAGTATATCAAGACGGCATCTGGGAACAAAGTCAGTCTCCAGTCAGT
GTTGTGTGGAAGCCAGAACATAGTTCTCAATGGCAAGACCATGTGATGAATGACTGTATTATCTGAGGGGATCTGGAAAA
GGTAAGAGTTGGACACCATTGTGTTGTGAAAAGTTGTAGTGTCATAAGGCCACCATTCAAGAAATTCAGCAAAGGCGTTG
AATTCTTTCCTTTACATATTGGGGACCATGTCTTTATTGAGGAAGAGTGTGTGGTCAACGCAGCTCAGATTGGTTCTTGC
ATTCATGTTGGCAAGAACTGTGTGATTGGGTGCCGGTGTTTATTGAAAGGCTGCTGCAAAATTCTTGACAACACAGCATT
ACCTCCAGAAACTGTGGTCCCACCATTCACTGTCTTCTCAGGCTGCCCAGGATGCTTCTCAGGAGAGCTCCTGGAGTGCA
CTCAGGAGCTAACGATTGATGTCACCAAGAGCTACTATCAGAAGTTTTTGCCCCTGACACAAGTC

Alignment

ORF - retro_ptro_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTI-VMNDCIIRGDLANVRVGRHCVVKSRSVI
          MELGELLYNKSEYI.TASGNKVS.QSVLCGSQNIVLNGKT..VMNDCII.GDL..VRVG.HCVVKS.SVI
Retrocopy MELGELLYNKSEYIKTASGNKVSLQSVLCGSQNIVLNGKTM<VMNDCII*GDLEKVRVGHHCVVKSCSVI

Parental  RPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETV
          RPPFKKFSKGV.FFPLHIGDHVFIEE.CVVNAAQIGS..HVGKNCVIG.RC.LK.CCKILDNT.LPPETV
Retrocopy RPPFKKFSKGVEFFPLHIGDHVFIEEECVVNAAQIGSCIHVGKNCVIGCRCLLKGCCKILDNTALPPETV

Parental  VPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLTQV
          VPPFTVFSGCPG.FSGEL.ECTQEL.IDVTKSYYQKFLPLTQV
Retrocopy VPPFTVFSGCPGCFSGELLECTQELTIDVTKSYYQKFLPLTQV

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	0.02 RPM	46.31 RPM
SRP007412_cerebellum	0.04 RPM	57.50 RPM
SRP007412_heart	0.03 RPM	39.03 RPM
SRP007412_kidney	0.00 RPM	56.38 RPM
SRP007412_liver	0.00 RPM	42.42 RPM
SRP007412_testis	0.11 RPM	74.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_220 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_220 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_260
Gorilla gorilla	retro_ggor_309
Pongo abelii	retro_pabe_405

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006410	1 retrocopy	retro_btau_1203,
Callithrix jacchus	ENSCJAG00000020623	1 retrocopy	retro_cjac_1687,
Homo sapiens	ENSG00000166847	1 retrocopy	retro_hsap_260,
Gorilla gorilla	ENSGGOG00000012834	1 retrocopy	retro_ggor_309,
Microcebus murinus	ENSMICG00000007806	1 retrocopy	retro_mmur_1082,
Myotis lucifugus	ENSMLUG00000012148	1 retrocopy	retro_mluc_140,
Mus musculus	ENSMUSG00000030868	2 retrocopies	retro_mmus_2733, retro_mmus_625,
Nomascus leucogenys	ENSNLEG00000012015	1 retrocopy	retro_nleu_863,
Pongo abelii	ENSPPYG00000007194	2 retrocopies	retro_pabe_1729, retro_pabe_405,
Pan troglodytes	ENSPTRG00000007891	1 retrocopy	retro_ptro_220 ,
Rattus norvegicus	ENSRNOG00000018048	2 retrocopies	retro_rnor_1351, retro_rnor_1847,