RetrogeneDB ID: retro_pabe_1582

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:21321017..21321862(-)
• Located in intron of: ENSPPYG00000009003

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0895L
• Ensembl ID: ENSPPYG00000007443
• Aliases: None
• Description: KIAA0895-like [Source:HGNC Symbol;Acc:34408]

Sequence

>retro_pabe_1582
ATGGTGCTGGACTCGGGGGCTCAGGCGTATGATCAGGTGCCCACCAGCCCACCTACCAGTCTCCTGTCCCTGCGTCATAG
GCTGAAGCCCTCAGACCGAGATGGGCCACCACTGTATCCCTGGTCTCAGTCCCTGGCCTTGCCCCTGGCTCTGGCAGTCC
CCCCAGCACTGCAGCCCCAGCCTGAGCAGCAGCCTTTCTCACAGATGCACCTGGGCCACCGTGGCCACATGCATGGCAGT
GAGAGCACCTACTCTGTAAATAGTACTGGCCGGCGGGGGCGTGGCACCCTGGGACGGCCTCCACCTGGACGGCGACGGAA
CCCAGGTGGGGGCACCCTGCGGCCCGCAGCCTCCCTGCCTCACATTGCTAAGACTCAAAGCGATGCAGGCCACAGTGCCA
GCAAGAGCCCCTGCATGTTGGTGGCCCTGCGGCCAACCAACGTGGACCGTGAGGGAGACAAATTCTTTCAGTCGCATTAC
ACCTACAATCCACAGTTCGAGTACCAGGAGCCCATGCCCACGGCTGTGCTGAAGTACTGCGAGGCCTCTGGACAGTTCAT
CCATCAGGCAGTTGGCATCATTGAGGCTGTTCTGGAGAAGTTTGGAAACCATGAACACTTTGAGGCTGCCACCGGGAGGC
GGCTGCTCACCAAGTGCCAGATATGGTCCATTGTGCGCAAATACATGCAGAAGGAGGGCTGCGTCGAAGAGGTTGTGGTG
CAGCTGAGTGAAGACCTGCTGTCCCAGGCAGTGATGATGGTAGAGAACAGCCGGCCCACATTGGCGGTCAACCTGACCAG
AGCCCGCCAGTACTGGCTGGAGGGATGCTGTGGCATGAAATAGGT

Alignment

ORF - retro_pabe_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.61 %
• Parental protein coverage: 67.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLDSGAQAYDQAPPSPPTSPPSLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQPEQQPFSQMH
          MVLDSGAQAYDQ.P.SPPTS..SLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQPEQQPFSQMH
Retrocopy MVLDSGAQAYDQVPTSPPTSLLSLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQPEQQPFSQMH

Parental  LGHRGHMRRSESTYSVNSTGRRGRGTLGRPPPGRGRNPGGGTLRPAASLPHIAKTQRDAGHIASKSPCML
          LGHRGHM..SESTYSVNSTGRRGRGTLGRPPPGR.RNPGGGTLRPAASLPHIAKTQ.DAGH.ASKSPCML
Retrocopy LGHRGHMHGSESTYSVNSTGRRGRGTLGRPPPGRRRNPGGGTLRPAASLPHIAKTQSDAGHSASKSPCML

Parental  VALRPTNMDRERDKFFQSHYTYNPQFEYQEPMPTAVLEKYCEASGQFIHQAVGIIEAVLEKFGTYEHFEA
          VALRPTN.DRE.DKFFQSHYTYNPQFEYQEPMPTAVL.KYCEASGQFIHQAVGIIEAVLEKFG..EHFEA
Retrocopy VALRPTNVDREGDKFFQSHYTYNPQFEYQEPMPTAVL-KYCEASGQFIHQAVGIIEAVLEKFGNHEHFEA

Parental  ATGGQLLTKCQIWSIVRKYMQKEGCVGEVVVQLSEDLLSQAVMMVENSRPTLAINLTGARQYWLE-GMLR
          ATG..LLTKCQIWSIVRKYMQKEGCV.EVVVQLSEDLLSQAVMMVENSRPTLA.NLT.ARQYWLE.GML.
Retrocopy ATGRRLLTKCQIWSIVRKYMQKEGCVEEVVVQLSEDLLSQAVMMVENSRPTLAVNLTRARQYWLE<GMLW

Parental  HEIG
          HEIG
Retrocopy HEIG

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	54.57 RPM
SRP007412_cerebellum	0.00 RPM	101.54 RPM
SRP007412_heart	0.00 RPM	4.06 RPM
SRP007412_kidney	0.10 RPM	12.83 RPM
SRP007412_liver	0.00 RPM	3.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1582 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1582 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1870

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196123	1 retrocopy	retro_hsap_1870,
Pongo abelii	ENSPPYG00000007443	2 retrocopies	retro_pabe_1582 , retro_pabe_1611,