RetrogeneDB ID: retro_hsap_1314

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:31487651..31488004(+)
• Located in intron of: ENSG00000196792

Retrocopy information

• Ensembl ID: ENSG00000258968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IFT20
• Ensembl ID: ENSG00000109083
• Aliases: None
• Description: intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]

Sequence

>retro_hsap_1314
ATGACACACCTCCTCCTGACTGTCACCGTCACTCCTTCAGAGCAGAGCTTCTCTAGGGAACTTGGATGCGAAACAACTAT
GGTAAAGGACATCCTGGCTGAAGAGGGACTGCACTTTGATGAGTTGAACAAGCTGTGGGTGTTGGACTCAGAGGTTACCC
AGCAGACCACAGAGCTCAAAGAAGAGTGCAAGAACTTTGCGGACAAAACTGGCCAGTTTCAGAAAACAGTTGGTGGTTTA
ATTGAGCTTGTTGATAAACTTGCAAAAAAAGCGTAAAATGCGAAGATGAGGGCCATGGTGCTCCGAACTTGCTCAAATCA
ATAGCAAAGCAGAGAGAAGCTCAACAACTTCAG

Alignment

ORF - retro_hsap_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 74.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTHLLLTATVTPSEQNSSREPGWETAMAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEECKDFVDKI
          MTHLLLT.TVTPSEQ..SRE.G.ET.M.KDIL.E.GLHFDELNKL.VLD.EVTQQT.ELKEECK.F.DK.
Retrocopy MTHLLLTVTVTPSEQSFSRELGCETTMVKDILAEEGLHFDELNKLWVLDSEVTQQTTELKEECKNFADKT

Parental  GQFQKIVGGLIELVDQLAKEAENEKMKAI-GARNLLKSIAKQREAQQQQ
          GQFQK.VGGLIELVD.LAK.A.N.KM.A..GA.NLLKSIAKQREAQQ.Q
Retrocopy GQFQKTVGGLIELVDKLAKKA*NAKMRAM<GAPNLLKSIAKQREAQQLQ

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	0.14 RPM	8.29 RPM
bodymap2_adrenal	0.16 RPM	8.39 RPM
bodymap2_brain	0.00 RPM	7.03 RPM
bodymap2_breast	0.23 RPM	11.36 RPM
bodymap2_colon	0.00 RPM	13.55 RPM
bodymap2_heart	0.06 RPM	3.45 RPM
bodymap2_kidney	0.00 RPM	11.44 RPM
bodymap2_liver	0.00 RPM	9.61 RPM
bodymap2_lung	0.00 RPM	12.99 RPM
bodymap2_lymph_node	0.00 RPM	15.08 RPM
bodymap2_ovary	0.00 RPM	9.08 RPM
bodymap2_prostate	0.00 RPM	15.45 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.66 RPM
bodymap2_testis	0.06 RPM	15.63 RPM
bodymap2_thyroid	0.00 RPM	15.44 RPM
bodymap2_white_blood_cells	0.00 RPM	9.37 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1314 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CUQ	POLR2A	14:31487388..31487892

EST

No EST(s) were mapped for retro_hsap_1314 retrocopy.

TSS

No TSS is located nearby retro_hsap_1314 retrocopy 5' end.

Lab

retro_hsap_1314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1314 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1026
Pongo abelii	retro_pabe_1097
Macaca mulatta	retro_mmul_2165
Callithrix jacchus	retro_cjac_687

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005111	2 retrocopies	retro_amel_1011, retro_amel_1337,
Bos taurus	ENSBTAG00000008110	1 retrocopy	retro_btau_257,
Callithrix jacchus	ENSCJAG00000012534	2 retrocopies	retro_cjac_2404, retro_cjac_687,
Cavia porcellus	ENSCPOG00000003153	1 retrocopy	retro_cpor_152,
Echinops telfairi	ENSETEG00000018843	2 retrocopies	retro_etel_1045, retro_etel_1181,
Homo sapiens	ENSG00000109083	1 retrocopy	retro_hsap_1314 ,
Gorilla gorilla	ENSGGOG00000004568	2 retrocopies	retro_ggor_1026, retro_ggor_1217,
Microcebus murinus	ENSMICG00000005074	1 retrocopy	retro_mmur_987,
Myotis lucifugus	ENSMLUG00000008709	2 retrocopies	retro_mluc_180, retro_mluc_1924,
Macaca mulatta	ENSMMUG00000019143	2 retrocopies	retro_mmul_2165, retro_mmul_2234,
Monodelphis domestica	ENSMODG00000019233	1 retrocopy	retro_mdom_681,
Mustela putorius furo	ENSMPUG00000014353	1 retrocopy	retro_mputfur_247,
Mus musculus	ENSMUSG00000001105	1 retrocopy	retro_mmus_3245,
Nomascus leucogenys	ENSNLEG00000001883	2 retrocopies	retro_nleu_1067, retro_nleu_1941,
Oryctolagus cuniculus	ENSOCUG00000007773	1 retrocopy	retro_ocun_438,
Otolemur garnettii	ENSOGAG00000003333	2 retrocopies	retro_ogar_1169, retro_ogar_72,
Ochotona princeps	ENSOPRG00000005826	6 retrocopies	retro_opri_110, retro_opri_1185, retro_opri_205, retro_opri_293, retro_opri_375, retro_opri_872,
Pongo abelii	ENSPPYG00000008087	2 retrocopies	retro_pabe_1097, retro_pabe_1322,
Sus scrofa	ENSSSCG00000023719	1 retrocopy	retro_sscr_315,
Ictidomys tridecemlineatus	ENSSTOG00000007554	1 retrocopy	retro_itri_713,
Tupaia belangeri	ENSTBEG00000005557	2 retrocopies	retro_tbel_180, retro_tbel_1954,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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