RetrogeneDB ID: retro_ptro_1258

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:22318101..22319036(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSPTRG00000008155
• Aliases: None
• Description: Pan troglodytes cytokine induced apoptosis inhibitor 1 (CIAPIN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246624]

Sequence

>retro_ptro_1258
ATGGCAGATTTTGGGATCTCTGCTGGCCAGTTTGTGGCAGTGGTCTGGGATAAGTCATCCCCAGTGGAGGCTCTGAAAGG
TCTGGTGGATGAGCTTCAAGGTTAACTGGCAATGAGGGCCATGGGTCTGTGGAAAACATGAACCAGCTGTTGCAGTCTGC
CCACAAAGAATCCAGCTTTGACATTATTTTGTCGGGTTTAGTCCCGGGAAGCACCACTCTGCACAGTGCTGAGATTTTGG
CTGAAATCACCCAGATCCTTCAGCCTGGTGGATGTCTTTTTCTGAAAGAGCCAGTAGAGACAGCTGTAGATAACAATAGC
AAAGTGAAGACAGCATCTAAGCTGTGTTCAGCCCTGACTCTTTCTGGTCTTGTGGAAGTGAAAGAGCTGCAACGGGAGCC
CCTAACCCCTGAGGAAATACAGTCTGTTCGAGAACACCTTGGTCATGAAAGTGACAGCCTGCTGTTTGTTCAGATCACAG
GCAAAAAACAAAACTTTGAAGTGGATTCTTCTAGTCAGCTTAAGTTTTCCATCACCAAGAAGTCTTCTCCTTCAGTGAAG
CCTGCTGTGGACCCTGCTGCTGCCAAGCTGTGGACCCTCTCAGCCAACGATATGGAGGACGACAGCATGGATCTCATTGA
CTCAGATGAGCTGCTGGATCCAGAAGATTTGAAGAAGCCAGATCCGGCTTCCCTGCAGGCTGCTTCTTGTGGGGAAGGGA
AAAAGAGGAAGGCCTGTAAGAACTGCACCTGTGGCCTTGCCACAGAACTGGAAAAAGAGAAGTCAAGGGAACAGATGAGC
TCCCAGCCCAAGTCGGCTTGTGGAAACTGCTACCTGGGTGATGCCTTCCGCTGTGCCAGCTGCCCCTACCTTGGGATGCC
AGCCTTCAAACCTGGGGAAAAGGCACTTCTGAGCAATAGCAATCTTCACGATGCC

Alignment

ORF - retro_ptro_1258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADFGISAGQFVAVVWDKSSPVEALKGLVDKLQA-LTGNEGRVSVENINQLLQSAHKESSFDIILSGLVP
          MADFGISAGQFVAVVWDKSSPVEALKGLVD.LQ..LTGNEG..SVEN.NQLLQSAHKESSFDIILSGLVP
Retrocopy MADFGISAGQFVAVVWDKSSPVEALKGLVDELQG<LTGNEGHGSVENMNQLLQSAHKESSFDIILSGLVP

Parental  GSTTLHSAEILAEIARILRPGGCLFLKEPVETAVDNNSKVKTASKLCSALTLSGLVEVKELQREPLTPEE
          GSTTLHSAEILAEI..IL.PGGCLFLKEPVETAVDNNSKVKTASKLCSALTLSGLVEVKELQREPLTPEE
Retrocopy GSTTLHSAEILAEITQILQPGGCLFLKEPVETAVDNNSKVKTASKLCSALTLSGLVEVKELQREPLTPEE

Parental  VQSVREHLGHESDNLLFVQITGKKPNFEVGSSRQLKFSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
          .QSVREHLGHESD.LLFVQITGKK.NFEV.SS.QLKFSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
Retrocopy IQSVREHLGHESDSLLFVQITGKKQNFEVDSSSQLKFSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS

Parental  MDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLAEELEKEKSREQMSSQPKSACGNCYL
          MDLIDSDELLDPEDLKKPDPASL.AASCGEGKKRKACKNCTCGLA.ELEKEKSREQMSSQPKSACGNCYL
Retrocopy MDLIDSDELLDPEDLKKPDPASLQAASCGEGKKRKACKNCTCGLATELEKEKSREQMSSQPKSACGNCYL

Parental  GDAFRCASCPYLGMPAFKPGEKVLLSDSNLHDA
          GDAFRCASCPYLGMPAFKPGEK.LLS.SNLHDA
Retrocopy GDAFRCASCPYLGMPAFKPGEKALLSNSNLHDA

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	0.34 RPM	36.18 RPM
SRP007412_cerebellum	0.68 RPM	27.10 RPM
SRP007412_heart	0.15 RPM	16.12 RPM
SRP007412_kidney	0.50 RPM	41.56 RPM
SRP007412_liver	0.23 RPM	22.75 RPM
SRP007412_testis	1.58 RPM	108.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1258 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1258 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1875
Gorilla gorilla	retro_ggor_1372
Pongo abelii	retro_pabe_1556

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012055	1 retrocopy	retro_cjac_2575,
Homo sapiens	ENSG00000005194	1 retrocopy	retro_hsap_1875,
Gorilla gorilla	ENSGGOG00000012402	1 retrocopy	retro_ggor_1372,
Macaca mulatta	ENSMMUG00000020472	1 retrocopy	retro_mmul_1719,
Monodelphis domestica	ENSMODG00000013522	1 retrocopy	retro_mdom_456,
Nomascus leucogenys	ENSNLEG00000002876	1 retrocopy	retro_nleu_1229,
Pongo abelii	ENSPPYG00000007388	2 retrocopies	retro_pabe_1260, retro_pabe_1556,
Pan troglodytes	ENSPTRG00000008155	1 retrocopy	retro_ptro_1258 ,