RetrogeneDB ID: retro_ptro_1428

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:31289938..31290489(-)
• Located in intron of: ENSPTRG00000013415

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1
• Ensembl ID: ENSPTRG00000004260
• Aliases: None
• Description: None

Sequence

>retro_ptro_1428
ATGGCTGCCGCTGGGGGCGCCCGGCTGCTGCGCGCCGCTTCTGCGGTCCTCGGCGACCCGGCCGGCCGGTGGCTGCACCA
CGCCGGGTCCCGCGCTGGAGCCAGCGGCCTGCTGAGGAGCCGGGGACCGGGCCGGAGCGCGGAGGCGAGACGGCCGCTGA
GCGTGTCGGCAGGGGCGCGAAGCAGCTCAGAAGATAAAGTGACAGTCCCCTTTATAAACTGTGATGGTGAAACATTAACA
ACCAAAGGAAAAGTTGGTGATTCTCTGCTAGACGTTGTGGTTGAAAATAATCTAGATATTGATGGCTTTGGTGCATGTGA
GGGAACTCTGGCTTGTTCAACCTGTCACCTCATCTTTGAAGGTCACATATATGAGAAGTTAGATGCAATCACTGATGAGG
AGAATCACATGCTCGATCTGGCATATGGACTAACAACAGATCACAGTTGGGCTGCCAAATCTGTTTGACAAAATCTATGG
ACAATATGACTGTTCGAGTGCCTGAAACAGTGGCTGATGCCAGACAATCCATTGATGTGGGCAAGACCTCC

Alignment

ORF - retro_ptro_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAGGARLLRAASAVLGGPGGRWLHHAGSRAGSSGLLRNRGPGGSAEASRSLSVSARARSSSEDKITVH
          MAAAGGARLLRAASAVLG.P.GRWLHHAGSRAG.SGLLR.RGPG.SAEA.R.LSVSA.ARSSSEDK.TV.
Retrocopy MAAAGGARLLRAASAVLGDPAGRWLHHAGSRAGASGLLRSRGPGRSAEARRPLSVSAGARSSSEDKVTVP

Parental  FINRDGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFEDHIYEKLDAITDEENDMLDL
          FIN.DGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFE.HIYEKLDAITDEEN.MLDL
Retrocopy FINCDGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFEGHIYEKLDAITDEENHMLDL

Parental  AYGLT-DRSRLGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS
          AYGLT..RS.LGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS
Retrocopy AYGLT<NRSQLGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS

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	0.13 RPM	7.02 RPM
SRP007412_cerebellum	0.04 RPM	7.64 RPM
SRP007412_heart	0.06 RPM	24.31 RPM
SRP007412_kidney	0.13 RPM	41.19 RPM
SRP007412_liver	0.07 RPM	38.50 RPM
SRP007412_testis	0.11 RPM	12.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1428 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1428 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2472
Pongo abelii	retro_pabe_1822

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 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,
Pan troglodytes	ENSPTRG00000010465	1 retrocopy	retro_ptro_267,