RetrogeneDB ID: retro_pabe_3653

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:71509381..71509787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHISA5
• Ensembl ID: ENSPPYG00000013902
• Aliases: None
• Description: protein shisa-5 [Source:RefSeq peptide;Acc:NP_001124981]

Sequence

>retro_pabe_3653
GGGTTTGGAGCTATGGGTGGCCATCAGCCTGACCATCTTTGTGCTGTCTGTCATCACTATCATCATTTGCTTCACCTGCT
CCTGCTGCTGCCTGTACAAGATGTGCCGCCAACCACGTCCGGTTGTCACCAGCATCACGTTCACCACTGTGGTGCACGCC
CCTTACACTCAGCCTCCAAGTGTGCCGCCCAGCTACCCTGGATCGAGCTACCAGGGCTACTACCCCATGCTCCCCCAGCC
AGGGATGCCAGCAGCACCCTACCCAACACAGTACCCACCACCTTACTCGGCCCAGCCCATGGGCCCGCCGGCCTACCACG
AGACCCTGGCTGGAGGAGCAACCGCGCCATACCCCAGGAGCCAGCCTCCTTACAACCTGGCCTACATATGTGCCCCGAAG
GCGGCT

Alignment

ORF - retro_pabe_3653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 64.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFGAT-LAVGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPS
          GFGA...A..LTIFVLSV.TIIICFTCSCCCLYK.CR.PRPVVT..T.TTVVHAPY.QPPSVPPSYPG.S
Retrocopy GFGAM>VAISLTIFVLSVITIIICFTCSCCCLYKMCRQPRPVVTSITFTTVVHAPYTQPPSVPPSYPGSS

Parental  YQGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYMDAPKAA
          YQGY..M.PQPGMPAAPYP.QYPPPY.AQPMGPPAYHETLAGGA.APYP.SQPPYN.AY..APKAA
Retrocopy YQGYYPMLPQPGMPAAPYPTQYPPPYSAQPMGPPAYHETLAGGATAPYPRSQPPYNLAYICAPKAA

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	0.22 RPM	111.47 RPM
SRP007412_cerebellum	0.00 RPM	38.91 RPM
SRP007412_heart	0.00 RPM	23.54 RPM
SRP007412_kidney	0.03 RPM	88.80 RPM
SRP007412_liver	0.03 RPM	70.51 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3653 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3653 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4706
Pan troglodytes	retro_ptro_3128
Callithrix jacchus	retro_cjac_4077

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077, retro_cjac_4152,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996, retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653 , retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,