RetrogeneDB ID: retro_pabe_16

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:46166229..46166994(+)
• Located in intron of: ENSPPYG00000011488

Retrocopy information

• Ensembl ID: ENSPPYG00000011496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000011492
• Aliases: None
• Description: None

Sequence

>retro_pabe_16
ATGGCTGCATCCACCATGTCCATCTGCTCCAGCGCTTGCACCGACTCTTGGCGGGTAGACGACTGCCCAGAGAGCTGCTA
TGAGCCCCCCTGCTGCACCCCCAGCTGCTGCGCCCTGGCCCCCTGTCTGACCCTGGTCTGCACCCCAGTGAGCTGTGTGT
CCAGTCCCTGCTGCCAGGCAGCCTGTGAGGCCAACCCCTGCCAATCAGGCTGCACCAGCTCCTGCACACCCTCATGCTAC
CAGCAGTCTAGCTGCCAGCCGGATTGCTGCACCTCCTCCCCCTGCCAGCAGGCCTGCTGTGTGCCTGTCTGCTGCAAGCC
CGTCTGCTGCGTGCCCATCTGTAACAAGCCTGTGTGCTTCGTGCCTACCTGCTCCGAGTCTTCCCCTTCATACTGCCAGC
AGTCTAGCTGCCAGCCAACTTGCTGCACCTCCTCCTCCTGCCAGCAGGCCTGCTGTGTGCCTGTCTGCTCCAAGTCCGTC
TGCTATGTGCCTGTGTGCTCTGGGGCTTCCACTTCATGCTGCCAGCAGTCTAGCTGCCAGCCTGCTAGCTGCACCACCTC
CTGCTGCAGACCCTCCTCCTCTGTGTCCCTCCTCTGCCACCCCGTGTGCAGGTCCACCTGCTGCGTGCCCATCCCCTCCT
GCGGTGCCTCTGCCTCCTCCTGCCAGCCCAGCTGCACGGCCTCCTGTGTTTCCTTCCTCTGCCGCCCCGTGTGCTCCCGC
CCCGCCTGCTACAGCCTCTGCTCTGGCCAGAAGTCCAGCTGCTGA

Alignment

ORF - retro_pabe_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.69 %
• Parental protein coverage: 69.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDSWQVDDCPESCCEPPCCTPSCCAPAPCLTLVCTPVSCVSSPCCQATCEPSP-QSGCTSSCTPSCCQQS
          .DSW.VDDCPESC.EPPCCTPSCCA.APCLTLVCTPVSCVSSPCCQA.CE..P.QSGCTSSCTPSC.QQS
Retrocopy TDSWRVDDCPESCYEPPCCTPSCCALAPCLTLVCTPVSCVSSPCCQAACEANPCQSGCTSSCTPSCYQQS

Parental  SCQQACCTSSPCQQSCCVPVCCKPVCCVPVCCKPVCCVPICSEDSSSCCQQSSCQPACCASSSCQQSCCV
          SCQ..CCTSSPCQQ.CCVPVCCKPVCCVP.C.KPVC.VP.CSE.S.S.CQQSSCQP.CC.SSSCQQ.CCV
Retrocopy SCQPDCCTSSPCQQACCVPVCCKPVCCVPICNKPVCFVPTCSESSPSYCQQSSCQPTCCTSSSCQQACCV

Parental  PVCCKPVCYVPSCSEDSSSCCQQSSCQPACCTSSPCQHTCCVPACCVPICCKPVCCVPTCSKDSSSCCQQ
          PVC.K.VCYVP.CS..S.SCCQQSSCQPA.CT.S.C.....V...C.P..C...CCVP..S...S....Q
Retrocopy PVCSKSVCYVPVCSGASTSCCQQSSCQPASCTTSCCRPSSSVSLLCHPV-CRSTCCVPIPSCGASASSCQ

Parental  SSCQPTCCASSSCQQSCCVPVC
          .SC....C.S..C...C..P.C
Retrocopy PSCTAS-CVSFLCRPVCSRPAC

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.03 RPM	0.07 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_16 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_16 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008415	1 retrocopy	retro_amel_1917,
Pongo abelii	ENSPPYG00000011492	3 retrocopies	retro_pabe_14, retro_pabe_15, retro_pabe_16 ,
Rattus norvegicus	ENSRNOG00000001218	2 retrocopies	retro_rnor_380, retro_rnor_382,