RetrogeneDB ID: retro_pabe_1260

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:66032488..66032929(+)
• 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_1260
TTTGAAGTGAGTTCTTCTAGTCAGCTTAAGCTTTCCATCACCAAGAAGTCATCTCCTTCAGTGAAGCTTGCTGGGTACCC
TGCTGCTGCCAAGCTGTGGACCCTCTCAGCCAATGATATGGAAGATGACAGCATGGATCTTATTGACTCAGAGGAGCTAC
TGGATCCAGAAGATTTGAAGAAGCCAGATCTGGCTTCCCTGCAGGCTGCTCCTTGTGGGGAAGGGAAAAAGAGGAAGACC
TGCCAGAGCTGCACCCGTGGGCTTGCTGAAGAACTGGAAAAAGAGAAGTCAAGGGAGCAGATGAGCTCCCAACCCAAGTC
AGCTTGTGGAAACTGCTATCTGGGCAATAGTTTCTGCTGTGCCGGCTGCCCCTACCTTGGGATACCAGCCTTCAAACCTG
GGGAAAAGGTGCTTCTGAGCAATAGCGGTCTTCACCATGCC

Alignment

ORF - retro_pabe_1260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 51.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FEVGSSRQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDSMDLIDSDELLDPEDLKKPDPASLRAA
          FEV.SS.QLKLSITKKSSPSVK.A..PAAAKLWTLSANDMEDDSMDLIDS.ELLDPEDLKKPD.ASL.AA
Retrocopy FEVSSSSQLKLSITKKSSPSVKLAGYPAAAKLWTLSANDMEDDSMDLIDSEELLDPEDLKKPDLASLQAA

Parental  SCGEGKKRKACKNCTCGLAEELEKQKSREQMSSQPKSACGNCYLGDAFRCASCPYLGMPAFKPGEKVLLS
          .CGEGKKRK.C..CT.GLAEELEK.KSREQMSSQPKSACGNCYLG..F.CA.CPYLG.PAFKPGEKVLLS
Retrocopy PCGEGKKRKTCQSCTRGLAEELEKEKSREQMSSQPKSACGNCYLGNSFCCAGCPYLGIPAFKPGEKVLLS

Parental  DSNLHDA
          .S.LH.A
Retrocopy NSGLHHA

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	28.59 RPM
SRP007412_cerebellum	0.00 RPM	19.94 RPM
SRP007412_heart	0.00 RPM	12.10 RPM
SRP007412_kidney	0.00 RPM	27.74 RPM
SRP007412_liver	0.00 RPM	17.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1260 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1260 has 0 orthologous retrocopies within eutheria group .

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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,