RetrogeneDB ID: retro_pabe_1611

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18_random:1984333..1985178(-)
• Located in intron of: None

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_1611
ATGGTGCTGGACTCGGGGGCTCAGGCGTATGATCAGGTGTCCACCAGCCCACCTACCAGTCTCCTGTCCCTGCGTCATAG
GCTGAAGCCCTCAGACCGAGATGGGCCACCGCTGTATCCCTGGTCTCAGTCCCTGGCCTTGCCCCTGGCTCTAGCAGTCC
CCCCAGCACTGCAGCCCCAGCCTAAGCAGCAGCCTTTCTCACAGATGCACCTGGGCCACCGTGGCCACATGCGTGGCAGT
GAGAGCACCTACTCTGTAAACAGTACTGGCCGGCGGGGGCGTGGCACCCTGGGACGGCCTCCACCTGGACGGCGACGGAA
CCCAGGTGGGGGCACCCTGCGGCCTACAGCCTCCCTGCCTCACATTGCTAAGACTCAAAGCGATGCAGACCACAGTGCCA
GCAAGAGCCCGTGCATGTTGGTGGCCCTGCGGCCAACCAACGTGGACCGTGAGGGAGACAAGTTCTTTCAGTCGCATTAC
ACCTACAATCCACAGTTCGAGTACCAGGAGCCCATGCCCACGGCTGTGCTGAAGTACTGAGAGGCCTCTGGACAGTTCAT
CCATCAGGCAGTTGGCATCATTGAGGCTGTTCTGGAGAAGTTTGGAAACCATGAACACTTTGAGGCTGCCACCGGGAGGC
GGCTGCTCACCAAGTGCCAGATATGGTCCATTGTGCGCAAATACATGCAGAAGGAGGGCTGCGTCGAAGAGGTTGTGGTG
CAGCTGAGTGAAGACCTGCTGTCCCAGGCAGTGATGATGGTGGAGAACAGCCGGCCCACATTGGCGGTCAACCTGACCAG
AGCCCGCCAGTACTGGCTGGAGGGATGCTGTGGCATGAAATAGGT

Alignment

ORF - retro_pabe_1611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.2 %
• Parental protein coverage: 67.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLDSGAQAYDQAPPSPPTSPPSLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQPEQQPFSQMH
          MVLDSGAQAYDQ...SPPTS..SLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQP.QQPFSQMH
Retrocopy MVLDSGAQAYDQVSTSPPTSLLSLRHRLKPSDRDGPPLYPWSQSLALPLALAVPPALQPQPKQQPFSQMH

Parental  LGHRGHMRRSESTYSVNSTGRRGRGTLGRPPPGRGRNPGGGTLRPAASLPHIAKTQRDAGHIASKSPCML
          LGHRGHMR.SESTYSVNSTGRRGRGTLGRPPPGR.RNPGGGTLRP.ASLPHIAKTQ.DA.H.ASKSPCML
Retrocopy LGHRGHMRGSESTYSVNSTGRRGRGTLGRPPPGRRRNPGGGTLRPTASLPHIAKTQSDADHSASKSPCML

Parental  VALRPTNMDRERDKFFQSHYTYNPQFEYQEPMPTAVLEKYCEASGQFIHQAVGIIEAVLEKFGTYEHFEA
          VALRPTN.DRE.DKFFQSHYTYNPQFEYQEPMPTAVL.KY.EASGQFIHQAVGIIEAVLEKFG..EHFEA
Retrocopy VALRPTNVDREGDKFFQSHYTYNPQFEYQEPMPTAVL-KY*EASGQFIHQAVGIIEAVLEKFGNHEHFEA

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	0.00 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_1611 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1611 has 0 orthologous retrocopies within eutheria group .

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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 ,