RetrogeneDB ID: retro_pabe_14

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:46232952..46233699(+)
• Located in intron of: ENSPPYG00000011488

Retrocopy information

• Ensembl ID: ENSPPYG00000011501
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_pabe_14
ATGTCCATCTGCTCCAGCGACCTGAGCTACGGCAGCCGCGTCTGCCTTGCTGGTTCCTGTGACTCTTGCTCTGACTCCTG
GCAGGTGGACGACTGCCAAGAGAGCTGCTGTGAGCCCCCCTGCTGCACCCCCAGCTGCTGCGCCCCGGCCGCCTGCCTGA
CCCTGGTCTGCACCCCAGTGAGCTGTGTGTCCAGCCCCTGCTGCCAGGCAGCCTGTGAGCCCAGCCCCTGCCAATCAGGC
TGCACCAGCTCCTGCACACCCTCATGCTGCCAGCAGTCTAGCTGCCAGCCGGCTTGCTCCTCCCCCTGCCAGCAGTCCTG
CTGCGTGCCTGTCTGCTGCAAGACTGTCTGCTGCAAGCCTGTGTGCTGTGTGCCCGTCTGCTGTGGGCCTTCTTCTTCAT
GTTGCCAGCAATCTAGCTGCCAGCCAGCTTGCTGCGTCTCCTCCCCGTGTCAACAGTCCTGCTGTGTGCCCGTCTGCTGC
AAGCCCATCTGCTGTGTGCCTATCTGCTCTGGGGCTTCCTCCCTGTGCTGCCAGCAGTCTAGGTGCCAGCCAGCTTGCTG
CACCACCTCCTGCTGCAGACCCTCCTCCTCCGTGTCCCTCCTCTGCCGCCCCGTGTGCAGACCCGCCTGCTGTGTGCCCG
TCCCCTCCTGCTGCGCCTCCACCTCCTCCTGCCAGCCAAGCTGCGGCTGCCTGGCCTCCTGCAGGTGCCTCCCCTGCCAC
CCCACATGTTCCCGCCTGGCCTGCTGA

Alignment

ORF - retro_pabe_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVCSSNLSYGSRVCLAGSCDSYSDSWQVDDCPESCCEPPCCTPSCCAPAPCLTLVCTPVSCVSSPCCQAT
          S.CSS.LSYGSRVCLAGSCDS.SDSWQVDDC.ESCCEPPCCTPSCCAPA.CLTLVCTPVSCVSSPCCQA.
Retrocopy SICSSDLSYGSRVCLAGSCDSCSDSWQVDDCQESCCEPPCCTPSCCAPAACLTLVCTPVSCVSSPCCQAA

Parental  CEPSP-QSGCTSSCTPSCCQQSSCQQACCTSSPCQQSCCVPVCCKPVCCVPVCCKPVCCVPICSEDSSSC
          CEPSP.QSGCTSSCTPSCCQQSSCQ.AC..SSPCQQSCCVPVCCK.VCC.PVCC.PVCC.P.....SS.C
Retrocopy CEPSPCQSGCTSSCTPSCCQQSSCQPAC--SSPCQQSCCVPVCCKTVCCKPVCCVPVCCGP----SSSCC

Parental  CQQSSCQPACCASSSCQQSCCVPVCCKPVCYVPSCSEDSSSCCQQSSCQPACCTSSPCQHTCCVPACCVP
          .QQSSCQPACC.SS.CQQSCCVPVCCKP.C.VP.CS..SS.CCQQS.CQPACCT.S.C.....V...C.P
Retrocopy -QQSSCQPACCVSSPCQQSCCVPVCCKPICCVPICSGASSLCCQQSRCQPACCTTSCCRPSSSVSLLCRP

Parental  ICCKPVCCVPTCSKDSSSCCQQSSCQPTCCASSSCQQSCCVPVCCKPVC
          ..C.P.CCVP..S.....C...SSCQP.C....SC....C.P.C....C
Retrocopy V-CRPACCVPVPS----CCASTSSCQPSCGCLASCRCLPCHPTCSRLAC

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	0.00 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_14 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_14 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,