RetrogeneDB ID: retro_pabe_2539

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:102160558..102161047(-)
• Located in intron of: ENSPPYG00000014941

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000000475
• Aliases: None
• Description: None

Sequence

>retro_pabe_2539
ATGGCAGCAGTGCTCTGTAGGCAGTGCCTCCCTTGGTCGTGGCTCTTCAGGAGAGACAGGCAGGACTGTGGCTGGCACTA
CTGTGCTGTGATTTGTGCAGAGCTGAAGAAGCCCCTGACCATTGAAGAGGTGGCCCCCCGCCCCGTCAAGCCTCACGAGG
TCAGAGTTGATGTCCATTTCTGTGGAGTTAACTTTGCTGATATTTTGGTCTGCCGTGGTCAGTATTAGGAAAGGCCCCAT
CTTCCCTTCACACCTGGAATGGAGTTTTCTGGGACAGTATTGGAGACAGACACAGATGTCAGCACAGTTAAAGAGGGAGA
TAGAGTTATTGGCATAAGAAACTTTAAATGTATGGCTGAAGAATGTGTCACTGATCAGAAAAACCTGCGGCAGATTCCAG
AAAAGTTCTCCCTACAAGAAGCTGCTGTCCTTTCTTTATGTTATGGCACTGCTATTTTTGCTCTTGAGCATTGGGCCTGT
ACCAAGCCT

Alignment

ORF - retro_pabe_2539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAAVLCRQCLPRAWVCRRAGQGSGWHYRAAICAELKKPLTVEEV-PLPVGPHEVRVDVHFCGVNFGDILI
          .AAVLCRQCLP..W..RR..Q..GWHY.A.ICAELKKPLT.EEV.P.PV.PHEVRVDVHFCGVNF.DIL.
Retrocopy MAAVLCRQCLPWSWLFRRDRQDCGWHYCAVICAELKKPLTIEEVAPRPVKPHEVRVDVHFCGVNFADILV

Parental  CRGQYQERPHLPFTPGMEFSGTVLETGTDVSTVKEGDRVIGIRNFSCMAEECVTDLKDPWQIPEKVFL-E
          CRGQY.ERPHLPFTPGMEFSGTVLET.TDVSTVKEGDRVIGIRNF.CMAEECVTD.K...QIPEK..L.E
Retrocopy CRGQY*ERPHLPFTPGMEFSGTVLETDTDVSTVKEGDRVIGIRNFKCMAEECVTDQKNLRQIPEKFSLQE

Parental  AAVLLITYGTAIFALEHQARTQP
          AAVL...YGTAIFALEH.A.T.P
Retrocopy AAVLSLCYGTAIFALEHWACTKP

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	1.00 RPM
SRP007412_cerebellum	0.00 RPM	0.24 RPM
SRP007412_heart	0.03 RPM	0.60 RPM
SRP007412_kidney	0.00 RPM	2.19 RPM
SRP007412_liver	0.03 RPM	1.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2539 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2539 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2105

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000014398	1 retrocopy	retro_ggor_2105,
Pongo abelii	ENSPPYG00000000475	1 retrocopy	retro_pabe_2539 ,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,