RetrogeneDB ID: retro_pabe_90

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:102778880..102779486(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020591
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB7A
• Ensembl ID: ENSPPYG00000013431
• Aliases: RAB7A, RAB7
• Description: ras-related protein Rab-7a [Source:RefSeq peptide;Acc:NP_001127416]

Sequence

>retro_pabe_90
ATGAGTGGGAAATCCCTGCTCTTAAAGGTCATTCTCTTGGGTGATGGTGGAGTTGGGAAAAGTTCGCTTATGAACCGTTA
TGTAACCAACAAATTTGACTCCCAGGCTTTTCACACCATAGGGGTAGAGTTCTTAAATCGAGATCTGGAGGTAGATGGAC
GCTTTGTAACCCTCCAGATCTGGGACACTGCAGGGCAGGAACGTTTCAAGAGCCTTAGGACACCCTTCTACAGGGGAGCA
GACTGCTGCCTCTTGACCTTCAGCGTGGATGATCGGCAGAGCTTCGAGAATCTTGGTAACTGGCAGAAAGAATTTATTTA
TTATGCGGATGTGAAGGACCCTGAGCATTTCCCCTTTGTAGTTCTGGGTAACAAGGTAGACAAAGAGGATAGGCAAGTGA
CTACTGAGGAGGCACAAGCCTGGTGCATGGAGAATGGGGATTACCCTTATTTAGAAACTAGTGCCAAAGATGATACTAAT
GTGACAGTGGCCTTTGAAGAAGCTGTCAGGCAGGTGTTGGCTGTAGAGGAACAGCTGGAGCATTGCATGTTGGGTCACAC
CATTGACTTGAACAGTGGCTCCAAAGCAGGGTCTTCGTGCTGTTAA

Alignment

ORF - retro_pabe_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.42 %
• Parental protein coverage: 86.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQS
          S.K..LLKVI.LGD.GVGK.SLMN.YV..KF..Q...TIG..FL.....VD.R.VT.QIWDTAGQERF.S
Retrocopy SGKSLLLKVILLGDGGVGKSSLMNRYVTNKFDSQAFHTIGVEFLNRDLEVDGRFVTLQIWDTAGQERFKS

Parental  LGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAW
          L...FYRGADCC.L.F.V.....F..L..W..EF...A...DPE.FPFVVLGNK.D.E.RQV.T..AQAW
Retrocopy LRTPFYRGADCCLLTFSVDDRQSFENLGNWQKEFIYYADVKDPEHFPFVVLGNKVDKEDRQVTTEEAQAW

Parental  CYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVE
          C......PY.ETSAK...NV..AF....R..L..E...E
Retrocopy CMENGDYPYLETSAKDDTNVTVAFEEAVRQVLAVEEQLE

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	5.25 RPM	181.19 RPM
SRP007412_cerebellum	9.97 RPM	103.12 RPM
SRP007412_heart	3.10 RPM	54.94 RPM
SRP007412_kidney	0.07 RPM	139.12 RPM
SRP007412_liver	0.03 RPM	98.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_90 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_90 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_90 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000365	1 retrocopy	retro_chof_13,
Felis catus	ENSFCAG00000022971	2 retrocopies	retro_fcat_661, retro_fcat_76,
Meleagris gallopavo	ENSMGAG00000007208	1 retrocopy	retro_mgal_7,
Myotis lucifugus	ENSMLUG00000008454	1 retrocopy	retro_mluc_1641,
Mustela putorius furo	ENSMPUG00000017333	1 retrocopy	retro_mputfur_1169,
Mus musculus	ENSMUSG00000079477	2 retrocopies	retro_mmus_3339, retro_mmus_3546,
Oryctolagus cuniculus	ENSOCUG00000001645	1 retrocopy	retro_ocun_259,
Pongo abelii	ENSPPYG00000003752	1 retrocopy	retro_pabe_1495,
Pongo abelii	ENSPPYG00000013431	1 retrocopy	retro_pabe_90 ,
Rattus norvegicus	ENSRNOG00000012247	1 retrocopy	retro_rnor_2779,
Sarcophilus harrisii	ENSSHAG00000016787	1 retrocopy	retro_shar_65,