RetrogeneDB ID: retro_hsap_94

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:3850045..3851023(+)
• Located in intron of: ENSG00000238158

Retrocopy information

• Ensembl ID: ENSG00000145945
• Aliases: FAM50B, D6S2654E, X5L
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM50A
• Ensembl ID: ENSG00000071859
• Aliases: FAM50A, 9F, DXS9928E, HXC-26, HXC26, XAP5
• Description: family with sequence similarity 50, member A [Source:HGNC Symbol;Acc:18786]

Sequence

>retro_hsap_94
ATGGCGCAGTACAAGGGCACCATGCGCGAGGCAGGCCGTGCCATGCACCTCCTCAAGAAGCGCGAAAGGCAGCGGGAGCA
GATGGAGGTGCTGAAGCAGCGCATCGCCGAGGAGACCATCCTCAAGTCGCAGGTGGACAAGAGGTTCTCGGCGCATTACG
ACGCCGTGGAGGCCGAGCTGAAGTCCAGCACGGTGGGCCTGGTGACCCTGAACGACATGAAGGCCCGGCAGGAGGCCCTG
GTCAGGGAGCGCGAGCGGCAGCTGGCCAAGCGCCAGCACCTGGAGGAGCAGCGGCTGCAGCAGGAGCGGCAGCGGGAGCA
GGAGCAGCGGCGCGAGCGCAAGCGTAAGATCTCCTGCCTGTCCTTTGCACTAGACGACCTCGATGACCAGGCCGACGCGG
CCGAGGCCAGGCGCGCCGGAAACCTGGGCAAGAACCCCGACGTGGACACCAGCTTCCTGCCAGACCGCGACCGCGAGGAG
GAGGAGAACCGGCTCCGAGAGGAGCTGCGCCAAGAGTGGGAGGCGCAGCGCGAGAAAGTGAAGGACGAGGAGATGGAGGT
CACCTTCAGCTACTGGGACGGCTCGGGCCACCGGCGCACGGTGCGGGTGCGCAAGGGCAACACGGTGCAGCAGTTCCTGA
AGAAGGCGCTGCAGGGGCTGCGCAAGGACTTCCTGGAGCTGCGCTCCGCCGGCGTGGAGCAGCTCATGTTCATCAAGGAG
GACCTCATCCTGCCGCACTACCACACCTTCTACGACTTCATCATCGCCAGGGCGAGGGGCAAGAGCGGGCCGCTCTTCAG
CTTCGATGTGCACGATGACGTGCGCCTGCTCAGCGACGCCACCATGGAGAAGGACGAGTCGCACGCGGGCAAGGTGGTGC
TGCGCAGCTGGTACGAGAAGAACAAGCACATCTTCCCCGCCAGCCGCTGGGAGGCCTATGACCCCGAGAAGAAGTGGGAC
AAGTACACCATCCGCTAA

Alignment

ORF - retro_hsap_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 54.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMRKGNTMQQ
          LGKNPDVDTSFLPDRDREEEENRLREELRQEWEA..EK.K.EE.E.TFSYWDGSGHRRTV..RKGNT.QQ
Retrocopy LGKNPDVDTSFLPDRDREEEENRLREELRQEWEAQREKVKDEEMEVTFSYWDGSGHRRTVRVRKGNTVQQ

Parental  FLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLSDAT
          FL.KAL..LRKDF.ELRSAGVEQLM.IKEDLI.PH.H.FYDFI...ARGKSGPLF.FDVHDDVRLLSDAT
Retrocopy FLKKALQGLRKDFLELRSAGVEQLMFIKEDLILPHYHTFYDFIIARARGKSGPLFSFDVHDDVRLLSDAT

Parental  VEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
          .EKDESHAGKVVLRSWYEKNKHIFPASRWE.YDPEKKWDKYTIR
Retrocopy MEKDESHAGKVVLRSWYEKNKHIFPASRWEAYDPEKKWDKYTIR

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	2.11 RPM	62.79 RPM
bodymap2_adrenal	2.99 RPM	52.40 RPM
bodymap2_brain	4.20 RPM	31.50 RPM
bodymap2_breast	3.27 RPM	38.81 RPM
bodymap2_colon	3.71 RPM	54.16 RPM
bodymap2_heart	2.75 RPM	17.85 RPM
bodymap2_kidney	3.81 RPM	39.69 RPM
bodymap2_liver	2.26 RPM	14.66 RPM
bodymap2_lung	1.27 RPM	32.14 RPM
bodymap2_lymph_node	2.06 RPM	50.27 RPM
bodymap2_ovary	3.78 RPM	36.51 RPM
bodymap2_prostate	5.47 RPM	41.81 RPM
bodymap2_skeletal_muscle	4.31 RPM	43.32 RPM
bodymap2_testis	6.82 RPM	34.24 RPM
bodymap2_thyroid	8.40 RPM	51.77 RPM
bodymap2_white_blood_cells	3.70 RPM	22.96 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_94 in 21 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	6:3849212..3849431
ENCFF002CFX	POLR2A	6:3849171..3849421
ENCFF002CGN	POLR2A	6:3849422..3849886
ENCFF002CHO	POLR2A	6:3849461..3849886
ENCFF002CJE	POLR2A	6:3849060..3849696
ENCFF002CJZ	POLR2A	6:3849517..3849771
ENCFF002CPG	POLR2A	6:3849410..3849900
ENCFF002CQA	POLR2A	6:3849404..3849974
ENCFF002CQC	POLR2A	6:3849420..3849900
ENCFF002CQE	POLR2A	6:3849548..3849723
ENCFF002CQG	POLR2A	6:3849386..3849910
ENCFF002CQI	POLR2A	6:3849442..3849878
ENCFF002CQK	POLR2A	6:3849524..3849786
ENCFF002CQO	POLR2A	6:3849589..3849810
ENCFF002CSY	POLR2A	6:3848965..3849655
ENCFF002CSY	POLR2A	6:3849302..3849992
ENCFF002CZC	POLR2A	6:3848596..3849136
ENCFF002CZC	POLR2A	6:3849392..3849932
ENCFF002CZQ	POLR2A	6:3849125..3849575
ENCFF002CZQ	POLR2A	6:3849408..3849858
ENCFF002CZW	POLR2A	6:3849286..3850036
ENCFF002DAV	POLR2A	6:3849030..3849574
ENCFF002DBO	POLR2A	6:3849472..3849856
ENCFF002DBP	POLR2A	6:3849510..3849840

EST

No EST(s) were mapped for retro_hsap_94 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_165528	257 libraries	110 libraries	783 libraries	494 libraries	185 libraries
TSS #2	TSS_165529	404 libraries	303 libraries	998 libraries	115 libraries	9 libraries
TSS #3	TSS_165530	1701 libraries	122 libraries	5 libraries	1 library	0 libraries

The graphical summary, for retro_hsap_94 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_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_94 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_103
Sus scrofa	retro_sscr_56

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94 ,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	4.32 RPM
CEU_NA11843	3.90 RPM
CEU_NA11930	1.56 RPM
CEU_NA12004	6.72 RPM
CEU_NA12400	4.59 RPM
CEU_NA12751	3.40 RPM
CEU_NA12760	8.89 RPM
CEU_NA12827	3.68 RPM
CEU_NA12872	2.91 RPM
CEU_NA12873	2.97 RPM
FIN_HG00183	2.36 RPM
FIN_HG00277	3.22 RPM
FIN_HG00315	3.89 RPM
FIN_HG00321	3.23 RPM
FIN_HG00328	4.76 RPM
FIN_HG00338	4.58 RPM
FIN_HG00349	5.80 RPM
FIN_HG00375	6.02 RPM
FIN_HG00377	4.44 RPM
FIN_HG00378	3.85 RPM
GBR_HG00099	5.55 RPM
GBR_HG00111	5.12 RPM
GBR_HG00114	6.65 RPM
GBR_HG00119	3.66 RPM
GBR_HG00131	2.47 RPM
GBR_HG00133	5.31 RPM
GBR_HG00134	7.47 RPM
GBR_HG00137	6.68 RPM
GBR_HG00142	4.58 RPM
GBR_HG00143	7.91 RPM
TSI_NA20512	7.80 RPM
TSI_NA20513	6.94 RPM
TSI_NA20518	6.36 RPM
TSI_NA20532	2.69 RPM
TSI_NA20538	3.18 RPM
TSI_NA20756	3.14 RPM
TSI_NA20765	4.43 RPM
TSI_NA20771	5.22 RPM
TSI_NA20786	6.56 RPM
TSI_NA20798	8.14 RPM
YRI_NA18870	5.52 RPM
YRI_NA18907	6.14 RPM
YRI_NA18916	5.30 RPM
YRI_NA19093	5.47 RPM
YRI_NA19099	2.13 RPM
YRI_NA19114	2.25 RPM
YRI_NA19118	5.84 RPM
YRI_NA19213	2.65 RPM
YRI_NA19214	5.76 RPM
YRI_NA19223	6.03 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).