RetrogeneDB ID: retro_pabe_1556

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:38393875..38394457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSPPYG00000007388
• Aliases: None
• Description: cytokine induced apoptosis inhibitor 1 [Source:HGNC Symbol;Acc:28050]

Sequence

>retro_pabe_1556
CTGACTCTTTCTAGTCTTGTGGAAGTGAAAGAGCTGCAGCGGGGGCCCCTAACCCCTGAGGAAATACAGTCTGTTCGAGA
ACACCTTGGTCATTAAAGTGACAGCCTGATATTTGTTCAGATCACAGGCAAAAAACCAAACTTTGAAGTGGGTTCTTCTA
GTCAGCTCAAGTTTTCCATCACCAAGAAGTCTTCTCCTTCAGTGAAGCCTGCTGTGGATCCTGCTGCTGCCAAGCTGTGG
ACCCTCTCAGCCAACAATATGGAGGACGACAGCATGGATCTCATTGACTCAGATGAGCTGCTGGATCCAGAAGATTTGAA
GAAGCCAGATCCGGCTTCCCTGTGGGCTGCTTCTTGTGGGGAAGGGAAAAAGAGGAAGGCCTGTAAGAACTGCACCTGTG
GCCTTGCCGAAGAACTGGAAAAAGAGAAGTCAAGGGAACAGATGAGCTCCAAACCCAAGTCGGCTTGTGGAAACTGCTAC
CTGGGCGATGCCTTCCGCTGTGCCAGCTGCCCCTACCTTGGGATGCCAGCCTTCAAACCTGGGGAAAAGGTGCTTCTGAG
CAATAGCAATCTTCACAATGCC

Alignment

ORF - retro_pabe_1556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 67.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFLKEPVETAVLQREPLTPEEVRSVREHLGHESDNLLFVQITGKKPNFEVGSSRQLKLSITKKSSPSVKP
          L.L...VE...LQR.PLTPEE..SVREHLGH.SD.L.FVQITGKKPNFEVGSS.QLK.SITKKSSPSVKP
Retrocopy LTLSSLVEVKELQRGPLTPEEIQSVREHLGH*SDSLIFVQITGKKPNFEVGSSSQLKFSITKKSSPSVKP

Parental  AVDPAAAKLWTLSANDMEDDSMDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLAEELE
          AVDPAAAKLWTLSAN.MEDDSMDLIDSDELLDPEDLKKPDPASL.AASCGEGKKRKACKNCTCGLAEELE
Retrocopy AVDPAAAKLWTLSANNMEDDSMDLIDSDELLDPEDLKKPDPASLWAASCGEGKKRKACKNCTCGLAEELE

Parental  KQKSREQMSSQPKSACGNCYLGDAFRCASCPYLGMPAFKPGEKVLLSDSNLHDA
          K.KSREQMSS.PKSACGNCYLGDAFRCASCPYLGMPAFKPGEKVLLS.SNLH.A
Retrocopy KEKSREQMSSKPKSACGNCYLGDAFRCASCPYLGMPAFKPGEKVLLSNSNLHNA

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	1.27 RPM	28.59 RPM
SRP007412_cerebellum	0.97 RPM	19.94 RPM
SRP007412_heart	0.15 RPM	12.10 RPM
SRP007412_kidney	1.06 RPM	27.74 RPM
SRP007412_liver	0.77 RPM	17.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1556 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1556 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1875
Pan troglodytes	retro_ptro_1258
Gorilla gorilla	retro_ggor_1372

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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,