RetrogeneDB ID: retro_hsap_4246

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:33968074..33968515(-)
• Located in intron of: ENSG00000137073

Retrocopy information

• Ensembl ID: ENSG00000226801
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_4246
ATGGAGACTTTGTACCGCGTCCCATTAGTGCTCAAATGTCCCAACCTGAAGCTGAAGAAGCCGACCAGGCTGCACATGCC
CTCGGCCATGACTATGTATGCCCTGGTGGTGGTGTCTTGCTTCCTCATCACCAGAGGAATAATTTATGATGTTATTGTTG
AACCTCAAAGTGTTGGCTCTGTGACCGATGAACATGGGCATCAGAGGCCAGTAGCTTTCTTGGTGTACAGAGTAAATGGA
CAGTATATTATGGAAGGACTTGCATCCAGCTTCCTGTTTACAATGGAGGGTTTAGGTTTCATAATCCTGTACCAATCGAA
TGCACCAAATATCCCAAAACCCAGTAGATTTCTTCTTCTATTCATTGGATTTGTCTGTGTCCTGTTGAGTTTTTTTATGG
CTAGAGTATTCATGAGAATGTAACTGCCGGGCAATCTGATA

Alignment

ORF - retro_hsap_4246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQR
          METLYRVP.LVL.CPNLKLKKP..LHMPSAMT.YALVVVS.FLIT.GIIYDVIVEP.SVGS.TDEHGHQR
Retrocopy METLYRVP-LVLKCPNLKLKKPTRLHMPSAMTMYALVVVSCFLITRGIIYDVIVEPQSVGSVTDEHGHQR

Parental  PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMR
          PVAFL.YRVNGQYIMEGLASSFLFTM.GLGFIIL..SNAPNIPK..RFLLLFIGFVCVLLSFFMARVFMR
Retrocopy PVAFLVYRVNGQYIMEGLASSFLFTMEGLGFIILYQSNAPNIPKPSRFLLLFIGFVCVLLSFFMARVFMR

Parental  MKLPGYLM
          M.LPG.L.
Retrocopy M*LPGNLI

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	0.08 RPM	38.62 RPM
bodymap2_adrenal	0.31 RPM	62.94 RPM
bodymap2_brain	0.14 RPM	11.16 RPM
bodymap2_breast	0.14 RPM	51.65 RPM
bodymap2_colon	0.08 RPM	71.12 RPM
bodymap2_heart	0.00 RPM	18.33 RPM
bodymap2_kidney	0.02 RPM	90.52 RPM
bodymap2_liver	0.00 RPM	106.95 RPM
bodymap2_lung	0.00 RPM	55.70 RPM
bodymap2_lymph_node	0.00 RPM	74.28 RPM
bodymap2_ovary	0.19 RPM	67.12 RPM
bodymap2_prostate	0.00 RPM	57.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.31 RPM
bodymap2_testis	0.15 RPM	62.23 RPM
bodymap2_thyroid	0.00 RPM	39.79 RPM
bodymap2_white_blood_cells	0.00 RPM	63.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4246 was not detected

EST

No EST(s) were mapped for retro_hsap_4246 retrocopy.

TSS

No TSS is located nearby retro_hsap_4246 retrocopy 5' end.

Lab

retro_hsap_4246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4246 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	0.06 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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