RetrogeneDB ID: retro_pabe_1729

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:27941503..27942049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN5
• Ensembl ID: ENSPPYG00000007194
• Aliases: None
• Description: dynactin subunit 5 [Source:RefSeq peptide;Acc:NP_001126840]

Sequence

>retro_pabe_1729
ATGGAGTTGGGTGAGCTGCTCTACAACAAGTCTGAGTATATCAAGACGGCATCTGGGAACAAAGCCAGTCTCCAGTCAGT
GTTGTGTGGAAGCCAGAACATAGTTCTCAATGGCAAGACCATTGTGATGAAAGACTGTGTTATCCGAGGGGTTCTGGAAA
ACGTAAGAATTGGACACCATTGTGTTGTGAAAAGTTGTAGTGTCATAAGGCCACCATTCAAGAAATTCAGCAAGGGTGTT
GAATTCTTTCCTTTACATATTGGGGACCATGTCTTTATTGAGGAAGAGTGTGTGGTCAACGCAGCTCAGATTGGTTATTG
CATTCATGTGGGCAAGAACTGTGTGATAGGGTGCCGGTGTTTGTTGAAAGACTGCTGCAAAATTCTTGACAACACAGCAT
TACCTCCAGAAACTGTGGTCCCACCATTCACTGTCTTCTCAGGCTGCCCAGGATGCTTCTCCGGAGAGCTCCTGGAGTGC
ACTCAGGAGCTGATGATTGATGTCACCAAGAGCTACTATCAGAAGTTTTTGCCCCTGACACAGGTC

Alignment

ORF - retro_pabe_1729 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRHCVVKSRSVIR
          MELGELLYNKSEYI.TASGNK.S.QSVLCGSQNIVLNGKTIVM.DC.IRG.L.NVR.G.HCVVKS.SVIR
Retrocopy MELGELLYNKSEYIKTASGNKASLQSVLCGSQNIVLNGKTIVMKDCVIRGVLENVRIGHHCVVKSCSVIR

Parental  PPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETVV
          PPFKKFSKGV.FFPLHIGDHVFIEE.CVVNAAQIG...HVGKNCVIG.RC.LKDCCKILDNT.LPPETVV
Retrocopy PPFKKFSKGVEFFPLHIGDHVFIEEECVVNAAQIGYCIHVGKNCVIGCRCLLKDCCKILDNTALPPETVV

Parental  PPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLTQI
          PPFTVFSGCPG.FSGEL.ECTQELMIDVTKSYYQKFLPLTQ.
Retrocopy PPFTVFSGCPGCFSGELLECTQELMIDVTKSYYQKFLPLTQV

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	48.21 RPM
SRP007412_cerebellum	0.00 RPM	54.36 RPM
SRP007412_heart	0.00 RPM	24.35 RPM
SRP007412_kidney	0.00 RPM	38.22 RPM
SRP007412_liver	0.00 RPM	25.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1729 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1729 has 0 orthologous retrocopies within eutheria group .

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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,