RetrogeneDB ID: retro_hsap_2630

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:33075348..33075963(+)
• Located in intron of: ENSG00000170266

Retrocopy information

• Ensembl ID: ENSG00000223899
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSG00000157020
• Aliases: SEC13, D3S1231E, SEC13L1, SEC13R, npp-20
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_hsap_2630
GGTATCATGGTGTCAGTAATTAACACTGTGGATACCTCCCATAAGGATATGATTTATGATGCCCAGATGGACTACTATGG
CACCCGCCTGGCAACCTGCTCATCAGAAAAATCCGTCAAAATCTTCAAAGTGCACAACAGAGGGCAGATCCTCATTGCCA
ACCTCAGAAGTCATGAGAGTCCTATGTGGCAAGTGGCCTGGGCTCACCCCACATATGGCAATATCCTGGCATTGTGCTCC
TATGATTGGAAAGTCATTATCTGGAAAGAGGAAAACGGCACCTGGGAGAAGACCCACGACCCCTCAGGATATGACTCCTC
CGTGAACTCTGTATGCTAGGTCCCCCATGACTACGGCCTGATCCTGGCCTGTAGGAGCTCAGATGGGGCCATCTTCCTGC
TGACTTATACAGGGGAAGGCCAATGGGAAGTGAAAAAGATCAACAACGCTTACACCATTGGCTGCAATGCCATCAGCTAG
GCCCCTGCTGTTGTACCTGGAAGCCTCATAGACCAGCTGTTCAGGCAGAAACCCAATTACATCAAGAAGTTTCCATCAGG
TGGCTGTGACAACCTCTTCAAGGATGGCCAGTGGAAGGAGAGCAGAAGCTGGAAG

Alignment

ORF - retro_hsap_2630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKMVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHP
          G.MVSVINTVDTSH.DMI.DAQMDYYGTRLATCSS..SVKIF.V.N.GQILIA.LR.HE.P.WQVAWAHP
Retrocopy GIMVSVINTVDTSHKDMIYDAQMDYYGTRLATCSSEKSVKIFKVHNRGQILIANLRSHESPMWQVAWAHP

Parental  MYGNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEG
          .YGNILA.CSYD.KVIIW.EENGTWEK.H...G.DSSVNSVC..PHDYGLILAC.SSDGAI.LLTYTGEG
Retrocopy TYGNILALCSYDWKVIIWKEENGTWEKTHDPSGYDSSVNSVC*VPHDYGLILACRSSDGAIFLLTYTGEG

Parental  QWEVKKINNAHTIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQWK
          QWEVKKINNA.TIGCNA.S.APAVVPGSLID....QKPNYIK.F.SGGCDNL.K.....E...WK
Retrocopy QWEVKKINNAYTIGCNAIS*APAVVPGSLIDQLFRQKPNYIKKFPSGGCDNLFKDGQWKESRSWK

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	0.02 RPM	39.60 RPM
bodymap2_adrenal	0.96 RPM	56.99 RPM
bodymap2_brain	0.12 RPM	23.86 RPM
bodymap2_breast	0.06 RPM	39.42 RPM
bodymap2_colon	0.02 RPM	32.25 RPM
bodymap2_heart	0.00 RPM	21.99 RPM
bodymap2_kidney	0.00 RPM	54.62 RPM
bodymap2_liver	0.00 RPM	50.04 RPM
bodymap2_lung	0.07 RPM	54.27 RPM
bodymap2_lymph_node	0.09 RPM	60.80 RPM
bodymap2_ovary	0.10 RPM	46.36 RPM
bodymap2_prostate	0.03 RPM	50.40 RPM
bodymap2_skeletal_muscle	0.00 RPM	69.99 RPM
bodymap2_testis	0.15 RPM	46.79 RPM
bodymap2_thyroid	0.00 RPM	44.84 RPM
bodymap2_white_blood_cells	0.00 RPM	44.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2630 was not detected

EST

No EST(s) were mapped for retro_hsap_2630 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_134228	332 libraries	490 libraries	890 libraries	108 libraries	9 libraries

The graphical summary, for retro_hsap_2630 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_2630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2630 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1774
Pongo abelii	retro_pabe_2333

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630 ,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 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).