RetrogeneDB ID: retro_hsap_1746

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:33332318..33332757(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSG00000198856
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_hsap_1746
ATGGAGACTTTGTACCATATCCCATTCTTAGTGCTCGAGTGTTCCAACCTGAAGTTGAAGAAGCCACCCTGGCTGCACAT
GCCATCAGCCATGACTGTGTATGCTCTGGTGGTGGTGTCTTACTTCCTCATGACTGGAGGAATAATTATATGATATTGTT
GAACCCCCAAGTATTGGCTGATGAACGTGGGCATCAGAGGCCAGTAGCTTTCTTGGCCTACAAAGTAAATGGACAGTATA
TTATGGAAGGATTTGCATCCAGCTTCCTGTTTACAATGGGAGGTTTAGGTTTCATAATGCTGGACCAGTCGAATGCACCA
AATATCCCAAAACTCAATCGATTTTTTTTCTTCTATTCATTGGATTCGTCTGTGTCCTACTGAGTTTTTTCATGGCTGGA
GTATTCATGTGAATGAAACTGCCGGGCTATCTGATGGGT

Alignment

ORF - retro_hsap_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGII-YDVIVEPPSVGSMTDEHGHQ
          METLY..PFLVLEC.NLKLKKPPWLHMPSAMTVYALVVVSYFL.TGGII.Y.....P.......DE.GHQ
Retrocopy METLYHIPFLVLECSNLKLKKPPWLHMPSAMTVYALVVVSYFLMTGGII<YMILLNPQV---LADERGHQ

Parental  RPVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNI-PKL-NRFLLLFIGFVCVLLSFFMARV
          RPVAFLAY.VNGQYIMEG.ASSFLFTMGGLGFI.LD.SNAPNI.PK......LLFIGFVCVLLSFFMA.V
Retrocopy RPVAFLAYKVNGQYIMEGFASSFLFTMGGLGFIMLDQSNAPNI<PKTQSXXXLLFIGFVCVLLSFFMAGV

Parental  FMRMKLPGYLMG
          FM.MKLPGYLMG
Retrocopy FM*MKLPGYLMG

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	0.97 RPM	38.62 RPM
bodymap2_adrenal	1.21 RPM	62.94 RPM
bodymap2_brain	0.63 RPM	11.16 RPM
bodymap2_breast	0.86 RPM	51.65 RPM
bodymap2_colon	0.73 RPM	71.12 RPM
bodymap2_heart	0.26 RPM	18.33 RPM
bodymap2_kidney	1.47 RPM	90.52 RPM
bodymap2_liver	0.15 RPM	106.95 RPM
bodymap2_lung	0.62 RPM	55.70 RPM
bodymap2_lymph_node	0.40 RPM	74.28 RPM
bodymap2_ovary	2.54 RPM	67.12 RPM
bodymap2_prostate	1.28 RPM	57.54 RPM
bodymap2_skeletal_muscle	1.89 RPM	7.31 RPM
bodymap2_testis	1.21 RPM	62.23 RPM
bodymap2_thyroid	1.45 RPM	39.79 RPM
bodymap2_white_blood_cells	1.30 RPM	63.63 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1746 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	17:33331280..33331424
ENCFF002CHO	POLR2A	17:33331138..33331385
ENCFF002CQO	POLR2A	17:33331009..33331539

EST

No EST(s) were mapped for retro_hsap_1746 retrocopy.

TSS

No TSS is located nearby retro_hsap_1746 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GAGGATCCCCAGTTTGAAGGG (21 nt long)
• Reverse primer: TGGAGGATTGGTACAGCCTTTAG (23 nt long)
• Anneling temperature: 58 °C
• (Expected) product size: 728
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1746 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011611	1 retrocopy	retro_btau_753,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Dasypus novemcinctus	ENSDNOG00000011172	2 retrocopies	retro_dnov_12, retro_dnov_1973,
Homo sapiens	ENSG00000198856	7 retrocopies	retro_hsap_1746 , retro_hsap_2013, retro_hsap_2972, retro_hsap_3598, retro_hsap_3686, retro_hsap_376, retro_hsap_4246,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222, retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Myotis lucifugus	ENSMLUG00000000478	2 retrocopies	retro_mluc_1366, retro_mluc_1511,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34,
Tursiops truncatus	ENSTTRG00000003446	1 retrocopy	retro_ttru_582,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.79 RPM
CEU_NA11843	0.40 RPM
CEU_NA11930	0.95 RPM
CEU_NA12004	0.84 RPM
CEU_NA12400	0.39 RPM
CEU_NA12751	0.90 RPM
CEU_NA12760	0.63 RPM
CEU_NA12827	0.85 RPM
CEU_NA12872	0.87 RPM
CEU_NA12873	0.77 RPM
FIN_HG00183	1.07 RPM
FIN_HG00277	1.11 RPM
FIN_HG00315	0.55 RPM
FIN_HG00321	1.03 RPM
FIN_HG00328	0.71 RPM
FIN_HG00338	0.57 RPM
FIN_HG00349	0.74 RPM
FIN_HG00375	0.59 RPM
FIN_HG00377	0.43 RPM
FIN_HG00378	0.83 RPM
GBR_HG00099	0.87 RPM
GBR_HG00111	0.34 RPM
GBR_HG00114	0.63 RPM
GBR_HG00119	0.69 RPM
GBR_HG00131	0.83 RPM
GBR_HG00133	0.63 RPM
GBR_HG00134	0.74 RPM
GBR_HG00137	0.63 RPM
GBR_HG00142	0.81 RPM
GBR_HG00143	0.45 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	1.18 RPM
TSI_NA20518	0.53 RPM
TSI_NA20532	1.36 RPM
TSI_NA20538	1.06 RPM
TSI_NA20756	0.49 RPM
TSI_NA20765	1.20 RPM
TSI_NA20771	0.45 RPM
TSI_NA20786	0.76 RPM
TSI_NA20798	0.69 RPM
YRI_NA18870	0.61 RPM
YRI_NA18907	1.07 RPM
YRI_NA18916	0.65 RPM
YRI_NA19093	0.78 RPM
YRI_NA19099	0.85 RPM
YRI_NA19114	0.58 RPM
YRI_NA19118	0.75 RPM
YRI_NA19213	0.65 RPM
YRI_NA19214	0.74 RPM
YRI_NA19223	0.97 RPM

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Indel association:

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