RetrogeneDB ID: retro_pabe_923

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:48454140..48454492(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C20orf27
• Ensembl ID: ENSPPYG00000010813
• Aliases: None
• Description: chromosome 20 open reading frame 27 [Source:HGNC Symbol;Acc:15873]

Sequence

>retro_pabe_923
TTTCTGAAGATCCTGCACAGGTATGAGATTACCTTTGCTCCGCCCCAGTGCACAGGCTGAGCAAGGACGTCCGCCAGACA
CTTGTCCCCAGCCCGCACCTGAAGCTTCTCAGCGTCCTACCCTTCCCTGAAGGTTATAGTGTCAAGTGCGAGTACTAGGC
GCACAAAGAGGGGGTCCTCAAAGAGGGGATGCTGCTAGTCTGGGAAGGTGGCACCGGCACCTGCGTGCGGGGGAGGTGCA
AGCCTGCATCATGGGCTGACAACACGGCACGTGCATGCTGCTGGATGGTGTCAAATGCGTGGGTGCCAAGCTGGAATACC
ACTCGGAGCACAGCGACTGTCACGGCTTTGAC

Alignment

ORF - retro_pabe_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 67.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLKILHRYEITFTLP-PVHRLSKDVREAPVPSLHLKLLSVVPVPEGYSVKCEYSAHKEGVLKEEILLACE
          FLKILHRYEITF..P.PVHRLSKDVR...VPS.HLKLLSV.P.PEGYSVKCEY.AHKEGVLKE..LL..E
Retrocopy FLKILHRYEITFAPP<PVHRLSKDVRQTLVPSPHLKLLSVLPFPEGYSVKCEY*AHKEGVLKEGMLLVWE

Parental  GGTGTCVR-VTVQARVMDRHHGTPMLLDGVKCVGAELEYDSEHSDWHGFD
          GGTGTCVR...VQA..M...HGT.MLLDGVKCVGA.LEY.SEHSD.HGFD
Retrocopy GGTGTCVR<GEVQACIMG*QHGTCMLLDGVKCVGAKLEYHSEHSDCHGFD

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	17.42 RPM
SRP007412_cerebellum	0.12 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	1.60 RPM
SRP007412_kidney	0.00 RPM	8.98 RPM
SRP007412_liver	0.00 RPM	9.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_923 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_923 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1114

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021194	1 retrocopy	retro_cjac_3292,
Homo sapiens	ENSG00000101220	2 retrocopies	retro_hsap_1114, retro_hsap_1673,
Gorilla gorilla	ENSGGOG00000016987	1 retrocopy	retro_ggor_871,
Macaca mulatta	ENSMMUG00000022079	1 retrocopy	retro_mmul_1578,
Nomascus leucogenys	ENSNLEG00000007653	1 retrocopy	retro_nleu_194,
Pongo abelii	ENSPPYG00000010813	1 retrocopy	retro_pabe_923 ,
Pan troglodytes	ENSPTRG00000013204	2 retrocopies	retro_ptro_1136, retro_ptro_685,