RetrogeneDB ID: retro_pabe_3562

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:4687611..4687959(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019993
• Aliases: None
• Description: None

Sequence

>retro_pabe_3562
CTCACAGCACACTTTCCCAGCCCAGCATGTGCCTCACCGCAACCCCCTAGGCCAAGCTCCTCAAGTGGGCCTCTCCAGGC
CCAGCTCTTCCTCCCGGTGGCCGCTGCAGGCCCAGACTGTTGTCAAGTTGGCCTGTCCAGGGTCAGCTCCTGCCTCCCGG
TGGCCTCTGCAGGCCCAGGTCGTCCTCAAGTCGGCCTCCACAGGCCCAGCTCCAGCCTCTCGGCGGCCTCTCCGGGTGCA
AAAGTTCCTCGAGTCAGCCTCTCCAGACCCAGCTCCTCCTGCCTCCCAGTGGCCTCTTTCAGCCCAGCCCAGCTCATGCC
CCCTGGCGGCCTTCCCAGGCCCTGCTTT

Alignment

ORF - retro_pabe_3562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.68 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWAQFFLPAASPGPIPAPTTSLDSAPAQL--PAALVGPQLPHGGLARLSSCPPKPSPGPKRRPQVSLPGP
          L.A.F..PA......P.P..S.....AQL..P.A..GP.....GL.R.SSC.P..S.GP.R.PQV.L..P
Retrocopy LTAHFPSPACASPQPPRPSSSSGPLQAQLFLPVAAAGPDCCQVGLSRVSSCLPVASAGPGR-PQVGLHRP

Parental  SSVLSAASPGAKLPQVSLSRPSSSCLPVASFGPAQLMALGGLPRPWF
          SS.LSAASPGAK.P.VSLSRPSSSCLPVASF.PAQLM..GGLPRP.F
Retrocopy SSSLSAASPGAKVPRVSLSRPSSSCLPVASFSPAQLMPPGGLPRPCF

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	0.11 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.20 RPM
SRP007412_liver	0.00 RPM	0.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3562 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032565	2 retrocopies	retro_cjac_2871, retro_cjac_3981,
Gorilla gorilla	ENSGGOG00000027883	1 retrocopy	retro_ggor_2012,
Pongo abelii	ENSPPYG00000019993	5 retrocopies	retro_pabe_1730, retro_pabe_3198, retro_pabe_3218, retro_pabe_3220, retro_pabe_3562 ,