RetrogeneDB ID: retro_pabe_2120

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:59929447..59929856(-)
• 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_2120
GGGTTTGGAGCGACCTTGGCCGTTGGCCTGACCATCTTTGTGCTGTCTGTAGTCACTATCATCATCTGCTTCACCTGCTC
CTGCTGCTGCCTTTACAAGATGTGCCACTGACCACGTCCGGTTGTCACCACCACCACATCTACCACTGTGGTGCATGCCC
CTTATCCTCAGCCTCCAAGTGTGCCGCCCAGCTACCCTGGACCAAGCTACCAGGGCTACCACACCATGCCACCTTAGCCA
GGGATGCCAGCAGCACCCTACCCAATGCAGCACCCACCACCTTTACCCAGCCCAGCCCATGGGCCCACCGGCCTACCACG
AGACCCTGGCTGGAGGAGCAGCCGCGCCCTACCCCACCAGCCAGGCTCCTTACAACCCGGCCTACATGGATGCCCCGAAG
GCGGCCCTC

Alignment

ORF - retro_pabe_2120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.16 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSY
          GFGATLAVGLTIFVLSVVTIIICFTCSCCCLYK.C..PRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSY
Retrocopy GFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKMCH*PRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSY

Parental  QGYHTMPPQPGMPAAPYPMQYPPP-YPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYMDAPKAAL
          QGYHTMPP.PGMPAAPYPMQ.PPP.YPAQPMGPPAYHETLAGGAAAPYP.SQ.PYNPAYMDAPKAAL
Retrocopy QGYHTMPP*PGMPAAPYPMQHPPP>YPAQPMGPPAYHETLAGGAAAPYPTSQAPYNPAYMDAPKAAL

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	0.28 RPM	111.47 RPM
SRP007412_cerebellum	0.12 RPM	38.91 RPM
SRP007412_heart	0.09 RPM	23.54 RPM
SRP007412_kidney	0.13 RPM	88.80 RPM
SRP007412_liver	0.18 RPM	70.51 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2120 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2120 has 0 orthologous retrocopies within eutheria group .

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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,