RetrogeneDB ID: retro_pabe_1841

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:26171065..26171472(+)
• Located in intron of: ENSPPYG00000011304

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1
• Ensembl ID: ENSPPYG00000003853
• Aliases: None
• Description: ferredoxin 1 [Source:HGNC Symbol;Acc:3638]

Sequence

>retro_pabe_1841
GGTGGGAGCACTGGGGTCAGCCAGAGATGAAACACGTCAGTGAAGGCCCAGAGCAGCTCAGAAGATAAAATAACAGTCCA
CTTTATAAACCAACAGTGAAACATTAACAAAGGAAAAGTTGATGACTCTCTGCTAGATGTTGTGGTTGAAAATAATGTAG
ATATTGATGGGTTTGTTGCATGGCAGGGAACCTTGGCTTGCTCTGTCACCTCAATTTTGAAAAGTACATATTTGAGAAGT
TAGACACAATCACTGAAAAGGAGACTGACATGCTTGATCTGGCATATGGACTGACAGACAGGTCAGAGTTGTATTGCCAA
ATCTGTTTGACAAAATCTATGGGCCATATGACTGTCTGAGTACCTGATGGAGTGGCCAGTGCCAGACAATCCACTGATAT
GGGCAAG

Alignment

ORF - retro_pabe_1841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGSAEASRSLSVSARARSSSEDKITVHFINRDGETLTTKGKVGDSLLDVVVENNLDIDGFGACE-GTLAC
          GGS...S.....S..A.SSSEDKITVHFIN........KGKV.DSLLDVVVENN.DIDGF.A...G.L..
Retrocopy GGSTGVSQR*NTSVKAQSSSEDKITVHFINQQ*NI--NKGKVDDSLLDVVVENNVDIDGFVAWQ<GNLGL

Parental  STCHLIFEDHIYEKLDAITDEENDMLDLAYGLTDRSRLGCQICLTKSMDNMTVRVPETVADARQSIDVGK
          ..CHL.FE..I.EKLD.IT..E.DMLDLAYGLTDRS.L.CQICLTKSM..MTV.VP..VA.ARQS.D.GK
Retrocopy -LCHLNFEKYIFEKLDTITEKETDMLDLAYGLTDRSELYCQICLTKSMGHMTV*VPDGVASARQSTDMGK

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	5.97 RPM
SRP007412_cerebellum	0.00 RPM	5.47 RPM
SRP007412_heart	0.06 RPM	8.82 RPM
SRP007412_kidney	0.07 RPM	15.28 RPM
SRP007412_liver	0.03 RPM	55.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1841 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1841 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2501
Gorilla gorilla	retro_ggor_1560
Pan troglodytes	retro_ptro_1452
Callithrix jacchus	retro_cjac_2028

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010395	1 retrocopy	retro_cjac_2028,
Homo sapiens	ENSG00000137714	2 retrocopies	retro_hsap_2472, retro_hsap_2501,
Gorilla gorilla	ENSGGOG00000022443	1 retrocopy	retro_ggor_1560,
Nomascus leucogenys	ENSNLEG00000007249	1 retrocopy	retro_nleu_1432,
Oryctolagus cuniculus	ENSOCUG00000017826	1 retrocopy	retro_ocun_1907,
Pongo abelii	ENSPPYG00000003853	2 retrocopies	retro_pabe_1822, retro_pabe_1841 ,
Pan troglodytes	ENSPTRG00000004260	2 retrocopies	retro_ptro_1428, retro_ptro_1452,