RetrogeneDB ID: retro_ptro_256

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:208144131..208144467(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSPTRG00000021075
• Aliases: None
• Description: Pan troglodytes iron-sulfur cluster assembly 1 homolog (S. cerevisiae) (ISCA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001242612]

Sequence

>retro_ptro_256
CTGCAGCCCACCGGGGCTGCCTTCACCCTGACACCGTCAGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGCCTGA
GCATGTAGGTGTAAATGCTGGTGTCTGAATCAGGGGCTGTAATGGCCTTTCTTATACTGTAGAATATACAAAGACAAAGG
GAGATTCTGATGAAGAAGTTATTCAAGATGGAGTCAGAGTATTCATTGAAAAGAAAGCCCAGCTAACACTTTTAGGAACA
GAAATGGACTATGTTGAAGACAAATTATCCAGTGAGTTTTTGTTCAATAACCCAAACATCAAAGGAACTTGTGGCTGTGG
AGAAACCTTTAATATT

Alignment

ORF - retro_ptro_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQPTRAALTLTPSAVNKIKQLLKDKPEHVGVKVGVRTRGCNGLSYTLEYTKTKGDSDEEVIQDGVRVFIE
          LQPT.AA.TLTPSAVNKIKQLLKDKPEHVGV..GV..RGCNGLSYT.EYTKTKGDSDEEVIQDGVRVFIE
Retrocopy LQPTGAAFTLTPSAVNKIKQLLKDKPEHVGVNAGV*IRGCNGLSYTVEYTKTKGDSDEEVIQDGVRVFIE

Parental  KKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFNI
          KKAQLTLLGTEMDYVEDKLSSEF.FNNPNIKGTCGCGE.FNI
Retrocopy KKAQLTLLGTEMDYVEDKLSSEFLFNNPNIKGTCGCGETFNI

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	38.84 RPM
SRP007412_cerebellum	0.00 RPM	15.67 RPM
SRP007412_heart	0.00 RPM	11.86 RPM
SRP007412_kidney	0.00 RPM	15.38 RPM
SRP007412_liver	0.00 RPM	5.04 RPM
SRP007412_testis	0.00 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_256 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_256 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1734

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Homo sapiens	ENSG00000135070	6 retrocopies	retro_hsap_1556, retro_hsap_1768, retro_hsap_1975, retro_hsap_2314, retro_hsap_317, retro_hsap_3329,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Macaca mulatta	ENSMMUG00000003399	3 retrocopies	retro_mmul_1230, retro_mmul_1365, retro_mmul_2211,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pan troglodytes	ENSPTRG00000021075	7 retrocopies	retro_ptro_1047, retro_ptro_1185, retro_ptro_1316, retro_ptro_1689, retro_ptro_2149, retro_ptro_256 , retro_ptro_2842,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,