RetrogeneDB ID: retro_ptro_2530

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:55923502..55924191(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAPCD2
• Ensembl ID: ENSPTRG00000021589
• Aliases: None
• Description: suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]

Sequence

>retro_ptro_2530
CCCGCCGAGGCGGCGCCCTGCCCCGTGGAACCGGAGCGGTCCCAGAGCGCGGCCCTGGAACAGAGCCCCAGCGCGGACGC
AGGTGCAGCGACCTGCAGGGCCTTGGAGGCAGACTCAGGGGATGCCCCGCGGGGCCCAGCGCCCGAGGAGAACGTCCGAG
TCACACCATCACCAGCGGCGTGGACTGCGGCCTGCTGAAGCAGATGAAGGAGCTGGAGCAGGAGAAGGAGGTGCTGCTGC
AGGGTTTGGAGATGATGGCGCGGGGCCGTGATTGGTACCAGCAGCAGCTGCAACGGGTGCAGGAGCGCCAGTGCCGCCTG
GGCCAGAGCAGAGCCAGCGCCGACTTTGGGGCCACGGGGAGCCCCCGCCCACTGGGGCGGCTACTGTCCAAGGTACAGGA
GGTGACCGGGTGCCTGGGGGAGCTGCTGGCTGCGGCCTGTGCCAGCTGGGCCCTGCCCACGTCCTCCTCCGGGCCCCCTG
CTGTGCCCTAAGGTCAACCTCGTCCCCGGGCTGTCAGCAGCAGACCATCCTCATGCTGAAGGAGCAGAACTGACTCCTTA
CCCAGGAGGCGACCGAGAAGAGTGAGTGCATCACGCAGCTGGAGCAGAAGTCAGCGCTCATTAAGCAGCTGTTTGAGGCC
CGCGCCCTGAGCCAGCAGGACGGGGGGGCCTCTGGACCCCACCTTCATC

Alignment

ORF - retro_ptro_2530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAEAAPCPAELERSQSAALEPSSSADAGAVACRALEADSGDARRAPR-ARGERRRHTITSGVDCGLLKQM
          PAEAAPCP.E.ERSQSAALE.S.SADAGA..CRALEADSGDA.R.P..ARGER..HTITSGVDCG.....
Retrocopy PAEAAPCPVEPERSQSAALEQSPSADAGAATCRALEADSGDAPRGPA<ARGERPSHTITSGVDCGXXXXX

Parental  KELEQEKEVLLQGLEMMARGRDWYQQQLQRVQERQRRLGQSRASADFGAAGSPRPLGRLLPKVQEVARCL
          .............LEMMARGRDWYQQQLQRVQERQ.RLGQSRASADFGA.GSPRPLGRLL.KVQEV..CL
Retrocopy XXXXXXXXXXXXXLEMMARGRDWYQQQLQRVQERQCRLGQSRASADFGATGSPRPLGRLLSKVQEVTGCL

Parental  GELLAAACASRALPPSSSGP-PCPALRSTSPPVWQQQTILMLKEQNRLLTQEVTEKSERITQLEQEKSAL
          GELLAAACAS.ALP.SSSGP.PC.ALRSTS.P..QQQTILMLKEQN.LLTQE.TEKSE.ITQLEQ.KSAL
Retrocopy GELLAAACASWALPTSSSGP<PCCALRSTSSPGCQQQTILMLKEQN*LLTQEATEKSECITQLEQ-KSAL

Parental  IKQLFEARALSQQD-GGPLDSTFI
          IKQLFEARALSQQD.GGPLD.TFI
Retrocopy IKQLFEARALSQQD>GGPLDPTFI

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	0.59 RPM
SRP007412_cerebellum	0.00 RPM	0.29 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.81 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.11 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2530 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2530 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3734

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734, retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867, retro_nleu_2939,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222, retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530 , retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,