RetrogeneDB ID: retro_hsap_2100

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:45223551..45223995(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231848
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRTCAP2
• Ensembl ID: ENSG00000163463
• Aliases: KRTCAP2, KCP2
• Description: keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:28942]

Sequence

>retro_hsap_2100
TTCTTGGTCAGAGGCGCCAATTTGACTCACAGGCAGGGCATGATGGTGGTGGGTACAGACACCTCACTGGCGATCTCCTC
CCTCCTGTCCCTGCTGCTCTTCACTGGGATGCAGATGTAGATCCATCAGCTGGCCTCCACCGAGTGGCTTACCATCCAGG
GTGGCCTGCATGGCTCAGGTCTCTTCGTGCTCTCCCTCACTGCCTTCAAGATTCTGGAGAATCTTGTGTTTGGCAAAGGA
TCCCAAGCAAAGACCTTCCCTGAGATTCTCCTGTGCCTCCTGTTGGCTCTCTTTGCATCTGGCCTCATCCACCGAGTCTG
TGTCACCACCTGCTTCATCTTCTCCGTGGTTGGTCTGTGCTACATCAACAAGATCTCCACTCTGTATCAGGCAGCAGCTG
CAGTCCTCACAGGACCTTGGCTCTTGCCAAGGTCACAGGCAAGA

Alignment

ORF - retro_hsap_2100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 91.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLARGAGWTHGRGMMVVGTGTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFN
          FL.RGA..TH..GMMVVGT.TSLA.SSLLSLLLF.GMQM...QLASTEWLTIQGGL.GSGLFV.SLTAF.
Retrocopy FLVRGANLTHRQGMMVVGTDTSLAISSLLSLLLFTGMQM*IHQLASTEWLTIQGGLHGSGLFVLSLTAFK

Parental  NLENLVFGKGFQAKIFPEILLCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQAAAPVLTPA
          .LENLVFGKG.QAK.FPEILLCLLLALFASGLIHRVCVTTCFIFS.VGL.YINKI.STLYQAAA.VLT..
Retrocopy ILENLVFGKGSQAKTFPEILLCLLLALFASGLIHRVCVTTCFIFSVVGLCYINKI-STLYQAAAAVLTGP

Parental  KVTGKSKKR
          .....S..R
Retrocopy WLLPRSQAR

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	61.82 RPM
bodymap2_adrenal	0.00 RPM	65.05 RPM
bodymap2_brain	0.00 RPM	12.73 RPM
bodymap2_breast	0.00 RPM	45.53 RPM
bodymap2_colon	0.00 RPM	44.28 RPM
bodymap2_heart	0.00 RPM	16.89 RPM
bodymap2_kidney	0.00 RPM	45.85 RPM
bodymap2_liver	0.00 RPM	45.39 RPM
bodymap2_lung	0.00 RPM	41.21 RPM
bodymap2_lymph_node	0.00 RPM	61.33 RPM
bodymap2_ovary	0.00 RPM	53.47 RPM
bodymap2_prostate	0.00 RPM	60.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	46.96 RPM
bodymap2_testis	0.02 RPM	66.99 RPM
bodymap2_thyroid	0.00 RPM	40.19 RPM
bodymap2_white_blood_cells	0.00 RPM	45.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2100 was not detected

EST

No EST(s) were mapped for retro_hsap_2100 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_123115	366 libraries	547 libraries	865 libraries	46 libraries	5 libraries

The graphical summary, for retro_hsap_2100 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_2100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2100 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1541
Gorilla gorilla	retro_ggor_1635
Pongo abelii	retro_pabe_1999
Macaca mulatta	retro_mmul_987
Callithrix jacchus	retro_cjac_1289

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100 ,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 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).