RetrogeneDB ID: retro_hsap_1625

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:14294213..14294666(+)
• Located in intron of: ENSG00000186260

Retrocopy information

• Ensembl ID: ENSG00000262470
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TVP23C
• Ensembl ID: ENSG00000175106
• Aliases: TVP23C, FAM18B2
• Description: trans-golgi network vesicle protein 23 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:30453]

Sequence

>retro_hsap_1625
ATGTTGCAGCAGGATAGTAATGATGACACTAAAGATGTTTCACTGTTTGATGCGGAAGAGGAGACGACTAATAGACCAAG
AAAAGTCAAAATCAGACATCCAGTAGCATCGTTTTTCCACTTATTCTTTCGAGTCAGTGCAATCATCGTCTGTCTTCTCT
GTGAATTGCTCAGCAGCAGCTTTATTACCTGTATGGTAACAATTATCTTGTTGTCATGTGACTTTTGGGCAGTGAAGAAT
ATCACAGGTAGACTAATGGTTGGCCTACGTTGGTGGAATCACGTTGATGAAGATGGAAAGAGCCACTGGGTGTTTGAATC
TAGAAAGGAGTCCTCTCAAGAGAATGAAACTGTGTCAGAGGCTGAATCAGGAATCTTTTGGTTGGGACTTGTTGCCTGTC
CAGTGCTGTGGGTGATACTTGCCTTCAGTGCACGCTTCTCCTTCAGAGTAAAA

Alignment

ORF - retro_hsap_1625 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 74.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQQDSNDDTEDVSLFDAEEETTNRPRKAKIRHPVASFFHLFFRVSAIIVCLLCELLSSSFITCMVTIIL
          MLQQDSNDDT.DVSLFDAEEETTNRPRK.KIRHPVASFFHLFFRVSAIIVCLLCELLSSSFITCMVTIIL
Retrocopy MLQQDSNDDTKDVSLFDAEEETTNRPRKVKIRHPVASFFHLFFRVSAIIVCLLCELLSSSFITCMVTIIL

Parental  LLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACSVLWVI
          L.SCDFWAVKN.TGRLMVGLRWWNH.DEDGKSHWVFESRKESSQEN.TVSEAES.IFWLGL.AC.VLWVI
Retrocopy L-SCDFWAVKNITGRLMVGLRWWNHVDEDGKSHWVFESRKESSQENETVSEAESGIFWLGLVACPVLWVI

Parental  FAFSALFSFTVK
          .AFSA.FSF.VK
Retrocopy LAFSARFSFRVK

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	2.82 RPM
bodymap2_adrenal	0.14 RPM	5.06 RPM
bodymap2_brain	0.40 RPM	3.38 RPM
bodymap2_breast	0.02 RPM	3.64 RPM
bodymap2_colon	0.00 RPM	2.18 RPM
bodymap2_heart	0.07 RPM	0.76 RPM
bodymap2_kidney	0.00 RPM	1.88 RPM
bodymap2_liver	0.00 RPM	0.59 RPM
bodymap2_lung	0.00 RPM	1.86 RPM
bodymap2_lymph_node	0.00 RPM	1.37 RPM
bodymap2_ovary	0.04 RPM	3.80 RPM
bodymap2_prostate	0.00 RPM	1.73 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.22 RPM
bodymap2_testis	0.32 RPM	4.90 RPM
bodymap2_thyroid	0.08 RPM	5.39 RPM
bodymap2_white_blood_cells	0.00 RPM	0.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1625 was not detected

EST

No EST(s) were mapped for retro_hsap_1625 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_48975	64 libraries	1 library	157 libraries	323 libraries	1284 libraries

The graphical summary, for retro_hsap_1625 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_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1625 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1344

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625 ,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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