RetrogeneDB ID: retro_hsap_3950

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:48076499..48076733(+)
• Located in intron of: ENSG00000248347

Retrocopy information

• Ensembl ID: ENSG00000248531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFA5
• Ensembl ID: ENSG00000128609
• Aliases: NDUFA5, B13, CI-13KD-B, CI-13kB, NUFM, UQOR13
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 [Source:HGNC Symbol;Acc:7688]

Sequence

>retro_hsap_3950
GGTGTGCTGAAGAAGACCACTGGCCTTGTGGGATTGGCTGTATGCAATACTCCACACGAGAGGCTAAGAATATTGTACAC
AAGGATTCTTGATGCTCTTGAGGAAATCCCTAAAAATGCAGCATATAGAAAGTATACAGAAGAGATTAGAAATGAGAAGC
TGGCTATGGTTAAAGCGGAACCAGAAGTTAAAAAATTAGAAGACCAACTTCAAGGCAGTCAATTAGAAGAAGTG

Alignment

ORF - retro_hsap_3950 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVLKKTTGLVGLAVCNTPHERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPDVKKLEDQL
          GVLKKTTGLVGLAVCNTPHERLRILYT.ILD.LEEIPKNAAYRKYTE.I.NEKLAMVKAEP.VKKLEDQL
Retrocopy GVLKKTTGLVGLAVCNTPHERLRILYTRILDALEEIPKNAAYRKYTEEIRNEKLAMVKAEPEVKKLEDQL

Parental  QGGQLEEV
          QG.QLEEV
Retrocopy QGSQLEEV

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
bodymap2_adipose	0.00 RPM	39.36 RPM
bodymap2_adrenal	0.00 RPM	65.87 RPM
bodymap2_brain	0.00 RPM	214.95 RPM
bodymap2_breast	0.00 RPM	79.03 RPM
bodymap2_colon	0.00 RPM	134.40 RPM
bodymap2_heart	0.00 RPM	210.44 RPM
bodymap2_kidney	0.00 RPM	172.48 RPM
bodymap2_liver	0.00 RPM	49.79 RPM
bodymap2_lung	0.00 RPM	61.34 RPM
bodymap2_lymph_node	0.00 RPM	46.49 RPM
bodymap2_ovary	0.00 RPM	70.77 RPM
bodymap2_prostate	0.00 RPM	102.33 RPM
bodymap2_skeletal_muscle	0.00 RPM	82.48 RPM
bodymap2_testis	0.00 RPM	102.07 RPM
bodymap2_thyroid	0.00 RPM	216.24 RPM
bodymap2_white_blood_cells	0.00 RPM	40.83 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3950 was not detected

EST

No EST(s) were mapped for retro_hsap_3950 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_184996	330 libraries	384 libraries	1020 libraries	77 libraries	18 libraries

The graphical summary, for retro_hsap_3950 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3950 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2682
Gorilla gorilla	retro_ggor_2654

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004512	2 retrocopies	retro_amel_1543, retro_amel_695,
Bos taurus	ENSBTAG00000009334	5 retrocopies	retro_btau_1258, retro_btau_1613, retro_btau_537, retro_btau_808, retro_btau_950,
Canis familiaris	ENSCAFG00000025112	4 retrocopies	retro_cfam_302, retro_cfam_445, retro_cfam_882, retro_cfam_921,
Callithrix jacchus	ENSCJAG00000017449	1 retrocopy	retro_cjac_65,
Felis catus	ENSFCAG00000027125	5 retrocopies	retro_fcat_1081, retro_fcat_1278, retro_fcat_244, retro_fcat_550, retro_fcat_799,
Homo sapiens	ENSG00000128609	10 retrocopies	retro_hsap_1065, retro_hsap_1687, retro_hsap_2671, retro_hsap_3218, retro_hsap_3627, retro_hsap_3950 , retro_hsap_3997, retro_hsap_4248, retro_hsap_745, retro_hsap_746,
Gorilla gorilla	ENSGGOG00000022922	9 retrocopies	retro_ggor_1264, retro_ggor_1864, retro_ggor_2185, retro_ggor_2447, retro_ggor_2654, retro_ggor_2683, retro_ggor_2848, retro_ggor_624, retro_ggor_840,
Loxodonta africana	ENSLAFG00000030971	1 retrocopy	retro_lafr_275,
Monodelphis domestica	ENSMODG00000015384	4 retrocopies	retro_mdom_1292, retro_mdom_1429, retro_mdom_1804, retro_mdom_525,
Mustela putorius furo	ENSMPUG00000006811	4 retrocopies	retro_mputfur_1151, retro_mputfur_1353, retro_mputfur_683, retro_mputfur_939,
Mus musculus	ENSMUSG00000023089	2 retrocopies	retro_mmus_2951, retro_mmus_853,
Otolemur garnettii	ENSOGAG00000033137	6 retrocopies	retro_ogar_1346, retro_ogar_1504, retro_ogar_1791, retro_ogar_2047, retro_ogar_2676, retro_ogar_649,
Pongo abelii	ENSPPYG00000017956	10 retrocopies	retro_pabe_1389, retro_pabe_2216, retro_pabe_2666, retro_pabe_2794, retro_pabe_2795, retro_pabe_2975, retro_pabe_3283, retro_pabe_3390, retro_pabe_3728, retro_pabe_887,
Pan troglodytes	ENSPTRG00000019637	10 retrocopies	retro_ptro_1141, retro_ptro_1800, retro_ptro_2235, retro_ptro_2452, retro_ptro_2682, retro_ptro_2714, retro_ptro_2888, retro_ptro_2937, retro_ptro_529, retro_ptro_725,
Rattus norvegicus	ENSRNOG00000005698	3 retrocopies	retro_rnor_1041, retro_rnor_2154, retro_rnor_2290,
Sus scrofa	ENSSSCG00000016607	2 retrocopies	retro_sscr_1029, retro_sscr_693,
Ictidomys tridecemlineatus	ENSSTOG00000027404	1 retrocopy	retro_itri_911,