RetrogeneDB ID: retro_pabe_2043

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:5521849..5522314(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSPPYG00000019339
• Aliases: None
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660]

Sequence

>retro_pabe_2043
TGCGCCCACTGTGTCCATGGAGAGAGGCTGAGGAGGCCGACCTCCGGCCCAAGGCACCGGGGCGCCGGGATGGCAAAGAT
GTTGGCTTCCTTAGTCCGGGCAACTGTCCAGGCTGTGAGCAAGAGGAAGCTGCAGCCCACCCGGGCAGCCCTCACCCTGA
CACCTTCAGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGCCTGAGCATGTAGGTGTAAAAGTTGGTGTCTGAACC
AGGGGCTGTAATGGCCTTTCTTATACTCTAGAATATACAAAGACAAAAGGAGATTCTGATGAAGAAGTTATTCAAGATGG
AGTCAGAGTATTCATCGAAAAGAAAGCACAGCTAACACTTTTAGGAGCAGAAATGGACTATGTTGAAGACAAATTATCCA
GTGAGTTTGTGTTCAATAACCCAAACATCAAAGGGACTTGTGGCTGTGGAGAAAGCTTTAATATT

Alignment

ORF - retro_pabe_2043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.84 %
• Parental protein coverage: 85.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CARCVHGERLRWATSGPRHRGAGTAKMSASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPE
          CA.CVHGERLR..TSGPRHRGAG.AKM.ASLVRATV.AVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPE
Retrocopy CAHCVHGERLRRPTSGPRHRGAGMAKMLASLVRATVQAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPE

Parental  HVGVKVGVRTRGCNGLSYTLEYTKTKGDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNN
          HVGVKVGV.TRGCNGLSYTLEYTKTKGDSDEEVIQDGVRVFIEKKAQLTLLG.EMDYVEDKLSSEFVFNN
Retrocopy HVGVKVGV*TRGCNGLSYTLEYTKTKGDSDEEVIQDGVRVFIEKKAQLTLLGAEMDYVEDKLSSEFVFNN

Parental  PNIKGTCGCGESFNI
          PNIKGTCGCGESFNI
Retrocopy PNIKGTCGCGESFNI

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	31.46 RPM
SRP007412_cerebellum	0.00 RPM	32.10 RPM
SRP007412_heart	0.03 RPM	18.54 RPM
SRP007412_kidney	0.00 RPM	11.54 RPM
SRP007412_liver	0.00 RPM	9.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2043 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2043 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2314
Pan troglodytes	retro_ptro_1689

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Canis familiaris	ENSCAFG00000001336	1 retrocopy	retro_cfam_1087,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Cavia porcellus	ENSCPOG00000011872	2 retrocopies	retro_cpor_1383, retro_cpor_768,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Equus caballus	ENSECAG00000011465	1 retrocopy	retro_ecab_936,
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,
Microcebus murinus	ENSMICG00000003889	1 retrocopy	retro_mmur_1399,
Myotis lucifugus	ENSMLUG00000001288	1 retrocopy	retro_mluc_1620,
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,
Nomascus leucogenys	ENSNLEG00000005129	5 retrocopies	retro_nleu_1674, retro_nleu_1725, retro_nleu_2330, retro_nleu_2618, retro_nleu_2782,
Oryctolagus cuniculus	ENSOCUG00000010945	1 retrocopy	retro_ocun_1685,
Otolemur garnettii	ENSOGAG00000015628	5 retrocopies	retro_ogar_1267, retro_ogar_1545, retro_ogar_2186, retro_ogar_2813, retro_ogar_935,
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,
Pteropus vampyrus	ENSPVAG00000004588	1 retrocopy	retro_pvam_956,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Sus scrofa	ENSSSCG00000010953	1 retrocopy	retro_sscr_558,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,
Tursiops truncatus	ENSTTRG00000004231	1 retrocopy	retro_ttru_1317,