RetrogeneDB ID: retro_hsap_2730

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:169649867..169651020(+)
• Located in intron of: ENSG00000187033

Retrocopy information

• Ensembl ID: ENSG00000244039
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSG00000116199
• Aliases: FAM20B, gxk1
• Description: family with sequence similarity 20, member B [Source:HGNC Symbol;Acc:23017]

Sequence

>retro_hsap_2730
ATACATCAACTGCCAAGCAGCGTTTCACTACTTGATCCCCTGAGGGCTTTTCACCGAATGATGACTGGCTTGTGGATGGA
GCTGTCACCCAAGTTGGACCACACGTTGCAGTCTTCCTAGGAGACTGCAGCCCAGTGGGTGGTTCCCCAGGAAGTGTACT
GTGAAGAGACACCAGAGCTGGGGGCAATCATGCATGCCATGGCCACCAAGCAAATTATTAAAGCTGATGTGGGTTATAAA
GGGACACAGCTGAAAGCCTTACTGATCCTTGAAAGGGAACAGAAAGTTGTTTTCGAACCTAAGTAGTATAGCCGAGACTA
TGTAGTGGAAGGGAACCATATGCCGGTTATGATAGACACAATGCGGAGGTAGCAGCCTTTCACTTGGACAGGATTGTGGG
TGTCCCAGAGCCCTGCTGATGGTGGGCAGATCCGTTCATCTTCAGACAGAGATCAAGCCTGTTACCATGGAGCAGCTGTT
GAGCCCCTTCCTAACTGTAGGACACAATACTTGTTTTTATGGGAAGTGTTATTACTACCGAGAAACAGAATCAGCTTGTG
CCGATGGAGACACAATGGAAAAATCTGTCACACTTTGGCTTCCAGATGTGTGGCCTCTCCAGAAACACTGACACCCGTGG
GCCAGGACTTACTGAAAAGGCAAATTGGCCAGGTGGGAGTATGATGAGCGCTACTGTGAGGCTGTGAAGAAAACGTCCCT
TTATGACTCTGGCCTGTGCCGCCTGGACACCATTAACACAGCTGTCTTTGATTACCTGATTGACAATGCTGACTGCCATT
ACTATAAGAACTTTCAAGATAATGAGGGCGCCAGTATGCTCATCCTTCTTGATAACAACAAAAGCTTTGGGAACCCCTTG
CTGGATGAAAGAAGCATTCTTTCCCCCCCTCTATCAGTGTGGCATCACTCAGGTGTCTACCTGGAACAGACGGAACTACC
TAAAGAATGGTGTGCTGAAGTCTACCTTAAAATCTGCCATGGCCCATGACCCCCTCTCCCCAGTGCTCTCTGATCCTCGT
CTGGACGCCATGGACCAGTGGCTCCTGAGTGTCCTGGCCACCGTGGAGCAGTGCACTGACCAGTTTGGGATGGACACTGT
ATGGTAGAAGACACAATGCCTTTCTCCCACTTG

Alignment

ORF - retro_hsap_2730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 94.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IDNLDTSAANREDQRAFHRMMTGLRVELAPKLDHTLQSPWEIAAQWVVPREVYPEETPELGAVMHAMATK
          I..L..S.......RAFHRMMTGL..EL.PKLDHTLQS..E.AAQWVVP.EVY.EETPELGA.MHAMATK
Retrocopy IHQLPSSVSLLDPLRAFHRMMTGLWMELSPKLDHTLQSS*ETAAQWVVPQEVYCEETPELGAIMHAMATK

Parental  KIIKADVGYKGTQLKALLILEGGQKVVFKPKRYSRDHVVEG-EPYAGYDRHNAEVAAFHLDRILGFH-RA
          .IIKADVGYKGTQLKALLILE..QKVVF.PK.YSRD.VVEG.EPYAGYDRHNAEVAAFHLDRI.G...RA
Retrocopy QIIKADVGYKGTQLKALLILEREQKVVFEPK*YSRDYVVEG<EPYAGYDRHNAEVAAFHLDRIVGVP<RA

Parental  PLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACADGDIMEGSVTLWLPDVWPLQ
          .L.VGR.V.L.TEIKPV..EQLLS.FLTVG.NTCFYGKCYY.RETE.ACADGD.ME.SVTLWLPDVWPLQ
Retrocopy LLMVGRSVHLQTEIKPVTMEQLLSPFLTVGHNTCFYGKCYYYRETESACADGDTMEKSVTLWLPDVWPLQ

Parental  KHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAVFDYLIGNADRHHYESFQDDEGA
          KH.HPW.RTY..GKLARWEYDE.YC.AVKKTS.YDSG...LD.I.TAVFDYLI.NAD.H.Y..FQD.EGA
Retrocopy KH*HPWARTY*KGKLARWEYDERYCEAVKKTSLYDSGLCRLDTINTAVFDYLIDNADCHYYKNFQDNEGA

Parental  SMLILLDNAKSFGNPSLDERSILA-PLYQCCIIRVSTWNRLNYLKNGVLKSALKSAMAHDPISPVLSDPH
          SMLILLDN.KSFGNP.LDERSIL..PLYQC.I..VSTWNR.NYLKNGVLKS.LKSAMAHDP.SPVLSDP.
Retrocopy SMLILLDNNKSFGNPLLDERSILS>PLYQCGITQVSTWNRRNYLKNGVLKSTLKSAMAHDPLSPVLSDPR

Parental  LDAVDQRLLSVLATVKQCTDQFGMDTV-LVEDRMPLSHL
          LDA.DQ.LLSVLATV.QCTDQFGMDTV..VED.MP.SHL
Retrocopy LDAMDQWLLSVLATVEQCTDQFGMDTV<MVEDTMPFSHL

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	111.02 RPM
bodymap2_adrenal	0.00 RPM	108.32 RPM
bodymap2_brain	0.00 RPM	98.26 RPM
bodymap2_breast	0.00 RPM	129.44 RPM
bodymap2_colon	0.00 RPM	172.36 RPM
bodymap2_heart	0.00 RPM	99.36 RPM
bodymap2_kidney	0.00 RPM	86.59 RPM
bodymap2_liver	0.00 RPM	32.83 RPM
bodymap2_lung	0.00 RPM	89.42 RPM
bodymap2_lymph_node	0.00 RPM	67.96 RPM
bodymap2_ovary	0.00 RPM	105.46 RPM
bodymap2_prostate	0.00 RPM	132.20 RPM
bodymap2_skeletal_muscle	0.00 RPM	92.74 RPM
bodymap2_testis	0.00 RPM	93.17 RPM
bodymap2_thyroid	0.00 RPM	96.27 RPM
bodymap2_white_blood_cells	0.00 RPM	68.95 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_2730 in 9 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	3:169650119..169650396
ENCFF002CPG	POLR2A	3:169649963..169650453
ENCFF002CQA	POLR2A	3:169649932..169650502
ENCFF002CQC	POLR2A	3:169649720..169650200
ENCFF002CQC	POLR2A	3:169649976..169650456
ENCFF002CQG	POLR2A	3:169649695..169650219
ENCFF002CQG	POLR2A	3:169649932..169650456
ENCFF002CQK	POLR2A	3:169649986..169650476
ENCFF002CQM	POLR2A	3:169649743..169650223
ENCFF002CQM	POLR2A	3:169649972..169650452
ENCFF002CQO	POLR2A	3:169649992..169650522
ENCFF002CQO	POLR2A	3:169649718..169650248
ENCFF002CZY	POLR2A	3:169649831..169650117
ENCFF002CZY	POLR2A	3:169650120..169650324

EST

No EST(s) were mapped for retro_hsap_2730 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_131526	1800 libraries	22 libraries	5 libraries	2 libraries	0 libraries

The graphical summary, for retro_hsap_2730 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_2730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2730 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1845
Pongo abelii	retro_pabe_2269

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730 ,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.30 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.28 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.18 RPM
FIN_HG00378	0.21 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.22 RPM
GBR_HG00143	0.32 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.25 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.35 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.25 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.22 RPM

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Indel association:

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