RetrogeneDB ID: retro_ptro_1602

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:60267047..60268704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL5
• Ensembl ID: ENSPTRG00000015989
• Aliases: None
• Description: kelch-like family member 5 [Source:HGNC Symbol;Acc:6356]

Sequence

>retro_ptro_1602
AGCCCGACGCGGACTTCCAATAGTAGTCAGACATTATCATCCTGTCATACTATGGAGCCATGTACATCAGATGAATTTTT
CCAAGCCCTTAATCATGCCGAGCAAACATTTAAAAAAATGGAAAACTATTTGAGACATAAACAGTTGTGCGATGTAATTT
TAGTCGCTGGTGATCGCAGAATTCCAGCTCACAGATTGGTGCTCTCCTCTGTCTCAGACTATTTTGCTGCCATGTTTACT
AATGATGTCAGAGAGGCAAGACAAGAAGAAATAAAAATGGAAGGTGTAGAACCAAATTCATTGTGGTCCTTGATCCAGTA
TGCTTATACAGGCCGCCTTGAATTAAAAGAAGATAATATTGAGTGCCTGTTATCTACAGCTTGCCTTCTTCAGCTTTCAC
AGGTTGTAGAAGCATGCTGTAAGTTTTTAATGAAACAGCTTCATCCATCCAACTGTCTTGGAATTCGTTCTTTTGCTGAT
GCCCAAGGTTGTACAGATTTGCATAAAGTGGCTCACAATTATACTATGGATCATTTCATGGAAGTAATCAGAAACCAGGA
ATTTGTATTATTACCAGCCAGTGAAATTGCAAAGCTCTTGGCTAGTGATGACATGAACATTCCTAATGAGGAGACAATAT
TGAATGCACTTCTTACTTGGGTCCGTCATGATTTGGAACAGAGACGGAAAGATCTAAGTAAACTTTTGGCTTATATTAGG
CTACCTCTTCTTGCACCACAGTTCCTGGCAGACATGGAAAATAATGCACTTTTTCGGGATGATATAGAATGTCAGAAACT
CATTATGGAAGCAATGAAGTACCATTTATTACCAGAGAGACGACCCATGTTACAAAGTCCTCGGACAAAACCTAGGAAGT
CAACTGTTGGTACATTATTTGCAGTTGGGGGAATGGATTCAACAAAAGGAGCAACAAGCATTTGAAAGTATGACTTCCGT
ACAAATATGTGGACTCCAGTAACAAATATGAATGGGAGGAGGCTACAGTCCGGTGGTCCAGTGCTAGATGACAAACTGTA
TGTGGTTGGAGGAAGAGATGGACTGAAGACTTTGAATACTGTAGAGTGCTACAACCCCAAAACAAAAACTTGGAGTGTGA
TGCCACCTATGTCCACACATAGACATGGCCTTGGTGTGGCTGTACTGGAAGGTCCCATGTATGCCGTAGGAGGACATGAT
GGCTGGAGCTATCTGAACACAGTGGAAAGATGGGACCCTCAGGCTCGCCAGTGGAATTTTGTTGCCACTATGTCTACCCC
TAGGAGTACAGTAGGTGTGGCAGTACTAAGTGGAAAACTTTATGCAGTTGGTGGTCGTGATGGAAGTTCTTGTCTCAAAT
CAGTAGAATGTTTTGATCCTCATACTACTAAGTGGACACTGTGTGCACAGATGTCAAAAAGGAGAGGTGGCGTAGGAGTG
ACGACCTGGAATGGACTGCTGTATGCTATAGGGGGGCACGATGCTCCCGCATCCAACTTGACTTCCAGACTCTCAGACTG
TGTGTAAAGATATGATCCCAAAACAGACATGTGGACTGCAGTAGCATCCATGAGCATCAGCAGAGATGCAGTCGGGGTCT
GTTTACTTGGTGATAAAGTTAATATGCTTGTTGGGGGGTTATGATGGACAGGCATAC

Alignment

ORF - retro_ptro_1602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.11 %
• Parental protein coverage: 72.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSCRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS
          S..RTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS
Retrocopy SPTRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS

Parental  VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC
          VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC
Retrocopy VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC

Parental  KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMEHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE
          KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTM.HFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE
Retrocopy KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMDHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE

Parental  ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER
          ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER
Retrocopy ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER

Parental  RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSIEKYDLRTNMWTPVANMNGRRLQFGVAVLDDKLYVVG
          RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI.KYD.RTNMWTPV.NMNGRRLQ.G..VLDDKLYVVG
Retrocopy RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI*KYDFRTNMWTPVTNMNGRRLQSGGPVLDDKLYVVG

Parental  GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF
          GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF
Retrocopy GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF

Parental  VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTNKWTLCAQMSKRRGGVGVTTWNGLLYAI
          VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHT.KWTLCAQMSKRRGGVGVTTWNGLLYAI
Retrocopy VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTTKWTLCAQMSKRRGGVGVTTWNGLLYAI

Parental  GGHDAPASNLTSRLSDCVERYDPKTDMWTAVASMSISRDAVGVCLLGDKL-YAVG-GYDGQAY
          GGHDAPASNLTSRLSDCV.RYDPKTDMWTAVASMSISRDAVGVCLLGDK....VG.GYDGQAY
Retrocopy GGHDAPASNLTSRLSDCV*RYDPKTDMWTAVASMSISRDAVGVCLLGDKVNMLVG>GYDGQAY

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	1.07 RPM	23.15 RPM
SRP007412_cerebellum	0.14 RPM	37.50 RPM
SRP007412_heart	0.09 RPM	21.66 RPM
SRP007412_kidney	0.10 RPM	29.42 RPM
SRP007412_liver	0.26 RPM	64.39 RPM
SRP007412_testis	0.21 RPM	41.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1602 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1602 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,
Pan troglodytes	ENSPTRG00000015989	1 retrocopy	retro_ptro_1602 ,