RetrogeneDB ID: retro_pabe_28

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:51974668..51975295(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000003441
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000004939
• Aliases: None
• Description: None

Sequence

>retro_pabe_28
ATGGCGCTGCTGGCCGAACACCTGCTGAAGCCGCTGCCGGCAGACAAGCAGATCAAGACCGGGCCCTTCCTCAAGGCGGT
GTCCCACCTGCCGCCCTTCTTCGATTGCCTTGGGTCCCCAGTGTTTACTCCCATCAAGGCAGACATAAGAGGCAACATCA
CGAAAATCAAAGCTGTGTACGACACCAACCCAGCCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGAAGAAAGAAATG
TATGGAGCAGAGCGGCCCAAAGTAGGGGCCACACTGGCGCTGATGTGGCTGAAAAGAGGCCTCCGCTTCATCCAGGTCTT
CCTCCAGAGCATCTGCGACGAGGAGCGGGATGAGAACCACCCCAACCTCATCCGCGTCAACGCCACCAAGGCCTACGAAA
TGGCCCTCAAGAAGTACCACGGCTGGACCGTGCAGAAGATCTTCCAGGCAGCACTGTACGCGGCCTCCTGTAAGTCCGAC
TTCCTGAAAGCGCTCTCCAAGGGGCAGAATGTGACGGAGGAGGAGTGCCTGGAGAAGATCCCCCTCTTCCTAGTCAACTA
CACGGCGACCATCGATGTCATCTACGAGACATACACCCAGATGAACGCTGAGCTTAACTACAAGGTG

Alignment

ORF - retro_pabe_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLGSPVFTPIKADISGNIMKIKTVYDTNPAKFRTLQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQ
          CLGSPVFTPIKADI.GNI.KIK.VYDTNPAKFRTLQNILEV.KEMYGAE.PKVGATLALMWLKRGLRFIQ
Retrocopy CLGSPVFTPIKADIRGNITKIKAVYDTNPAKFRTLQNILEVKKEMYGAERPKVGATLALMWLKRGLRFIQ

Parental  VFLQSICDGERDENHPNLIRVNATKAYEMALKKYHGWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEEE
          VFLQSICD.ERDENHPNLIRVNATKAYEMALKKYHGW.VQKIFQAALYAA..KSDFLKALSKGQNVTEEE
Retrocopy VFLQSICDEERDENHPNLIRVNATKAYEMALKKYHGWTVQKIFQAALYAASCKSDFLKALSKGQNVTEEE

Parental  CLEKIRLFLVNYTATIDVIYEMYTQMNAELNYKV
          CLEKI.LFLVNYTATIDVIYE.YTQMNAELNYKV
Retrocopy CLEKIPLFLVNYTATIDVIYETYTQMNAELNYKV

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	0.17 RPM	9.07 RPM
SRP007412_cerebellum	0.12 RPM	17.15 RPM
SRP007412_heart	0.09 RPM	6.08 RPM
SRP007412_kidney	0.53 RPM	30.79 RPM
SRP007412_liver	0.28 RPM	13.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_28 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_28 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_28 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_755
Pan troglodytes	retro_ptro_41

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034092	1 retrocopy	retro_cjac_1284,
Echinops telfairi	ENSETEG00000016033	1 retrocopy	retro_etel_1197,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Macaca mulatta	ENSMMUG00000022761	1 retrocopy	retro_mmul_2261,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28 ,
Pongo abelii	ENSPPYG00000017682	1 retrocopy	retro_pabe_919,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,
Rattus norvegicus	ENSRNOG00000001192	1 retrocopy	retro_rnor_2465,
Ictidomys tridecemlineatus	ENSSTOG00000004484	1 retrocopy	retro_itri_973,