RetrogeneDB ID: retro_pabe_2956

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:56244664..56245046(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCU
• Ensembl ID: ENSPPYG00000004920
• Aliases: None
• Description: iron-sulfur cluster scaffold homolog (E. coli) [Source:HGNC Symbol;Acc:29882]

Sequence

>retro_pabe_2956
AAGATTGTTGATTTCTATGAAAATCCTACAAATGTGGGGTCCCATGATAAGACATCTAAAAATATTGAAATTGCATTGGT
GTGGGCTTCAGCATGAGGTGATAAAATACAGATTCAAGTGGACAAAAAGGGGAAGATTGTGGACATAAGGTTTAAAATAT
CTGGCTGCAGTTCTGCAGTTGCCTCCAGCCCGTTAGCCACTGACAGGGTGAAAAAGAATATGATAGAGGAAACCTATACC
CTCAAAAACACAGACATCACCAAGGAGCCCTGCCTTCCTCTTGTGAAACTGCCTGCTCCCTGCTGGCTGAAGATGCAACT
AAGGCCACCTGGCTGGTTACACACTAAAATAAGGACCCGAGAAAGGAGAGGTGGAGAAGAAA

Alignment

ORF - retro_pabe_2956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.91 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATE
          K.VD.YENP.NVGS.DKTSKN....LV.A.A.GD..K.QIQVD.KGKIVD.RFK..GC.SA.ASS.LAT.
Retrocopy KIVDFYENPTNVGSHDKTSKNIEIALVWASA*GD--KIQIQVDKKGKIVDIRFKISGCSSAVASSPLATD

Parental  WVKGKTVEEALTIKNTDIAKELCLPPVKL-HCSMLAEDAIKAA-LADYKLKQEPKKGEAEKK
          .VK....EE..T.KNTDI.KE.CLP.VKL..CS.LAEDA.KA..LA.Y.LK..P.KGE.EKK
Retrocopy RVKKNMIEETYTLKNTDITKEPCLPLVKL<ACSLLAEDATKAT<LAGYTLK*GPEKGEVEKK

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	169.19 RPM
SRP007412_cerebellum	0.00 RPM	88.89 RPM
SRP007412_heart	0.00 RPM	74.27 RPM
SRP007412_kidney	0.00 RPM	106.40 RPM
SRP007412_liver	0.00 RPM	38.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2956 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2956 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3596
Gorilla gorilla	retro_ggor_2426

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016405	3 retrocopies	retro_amel_1338, retro_amel_755, retro_amel_902,
Bos taurus	ENSBTAG00000011787	3 retrocopies	retro_btau_378, retro_btau_646, retro_btau_648,
Canis familiaris	ENSCAFG00000011324	4 retrocopies	retro_cfam_388, retro_cfam_390, retro_cfam_599, retro_cfam_686,
Choloepus hoffmanni	ENSCHOG00000011773	2 retrocopies	retro_chof_229, retro_chof_2698,
Callithrix jacchus	ENSCJAG00000015374	2 retrocopies	retro_cjac_1584, retro_cjac_1644,
Cavia porcellus	ENSCPOG00000010986	1 retrocopy	retro_cpor_1201,
Equus caballus	ENSECAG00000019879	3 retrocopies	retro_ecab_359, retro_ecab_753, retro_ecab_849,
Felis catus	ENSFCAG00000014044	2 retrocopies	retro_fcat_1769, retro_fcat_471,
Homo sapiens	ENSG00000136003	2 retrocopies	retro_hsap_3596, retro_hsap_468,
Gorilla gorilla	ENSGGOG00000011579	2 retrocopies	retro_ggor_2426, retro_ggor_446,
Loxodonta africana	ENSLAFG00000007170	2 retrocopies	retro_lafr_609, retro_lafr_728,
Microcebus murinus	ENSMICG00000013067	4 retrocopies	retro_mmur_1359, retro_mmur_558, retro_mmur_636, retro_mmur_81,
Macaca mulatta	ENSMMUG00000017126	1 retrocopy	retro_mmul_572,
Monodelphis domestica	ENSMODG00000002828	1 retrocopy	retro_mdom_1924,
Mus musculus	ENSMUSG00000025825	2 retrocopies	retro_mmus_1806, retro_mmus_3317,
Nomascus leucogenys	ENSNLEG00000006797	2 retrocopies	retro_nleu_299, retro_nleu_884,
Oryctolagus cuniculus	ENSOCUG00000016305	1 retrocopy	retro_ocun_637,
Procavia capensis	ENSPCAG00000007604	2 retrocopies	retro_pcap_257, retro_pcap_86,
Pongo abelii	ENSPPYG00000004920	3 retrocopies	retro_pabe_1753, retro_pabe_266, retro_pabe_2956 ,
Tupaia belangeri	ENSTBEG00000001086	3 retrocopies	retro_tbel_1987, retro_tbel_2588, retro_tbel_545,
Tarsius syrichta	ENSTSYG00000013952	2 retrocopies	retro_tsyr_1484, retro_tsyr_98,
Tursiops truncatus	ENSTTRG00000004036	1 retrocopy	retro_ttru_1720,
Xenopus tropicalis	ENSXETG00000027428	1 retrocopy	retro_xtro_66,