RetrogeneDB ID: retro_hsap_3847

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:55327504..55327949(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230564
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALM1
• Ensembl ID: ENSG00000198668
• Aliases: CALM1, CALML2, CAMI, CPVT4, DD132, PHKD, caM
• Description: calmodulin 1 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1442]

Sequence

>retro_hsap_3847
ATGGCTGATCAGCTGACCAAAGAACAGATTGCTGAATTCGAGGAAGCTTTCTCCCTGTCCTATAAAGATAGTAATGGCAC
TATCACAACAAAGGAACTTGGAACCATCATGAGGTCACTGGGTCAGAACCCAGCAGAATCTGAATTGCAGGACATGATCA
ATGAAGTGGATTCTGATGGCAATGACACCATTTAATTCCTCGAATTTTTGACCATGATGGCTAGAAAAATGAAAGACACA
TATAGTGAAGAAGAAATCGTGAGGTATTCCAGTCTTTGACGATAGTGGCAAAGGTTACATCAGTGCAGCAGAACTACGTC
ATGTCATGACAAACTTAGGAGAAAAACTAATAGATGAAGAAGTAGATGAAATGATGACAGAAGCAGATATTGATGGAGAC
AGACAAGTTGATTATGAAGAATTAATACAGATGATGACTGCAAAA

Alignment

ORF - retro_hsap_3847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
          MADQLT.EQIAEF.EAFSL..KD..GTITTKELGT.MRSLGQNP.E.ELQDMINEVD.DGN.TI.F.EFL
Retrocopy MADQLTKEQIAEFEEAFSLSYKDSNGTITTKELGTIMRSLGQNPAESELQDMINEVDSDGNDTI*FLEFL

Parental  TMMARKMKDTDSEEEI-REAFR-VFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVN
          TMMARKMKDT.SEEEI.RE.F..VFD..G.GYISAAELRHVMTNLGEKL.DEEVDEM..EADIDGD.QV.
Retrocopy TMMARKMKDTYSEEEI<REVFQ<VFDDSGKGYISAAELRHVMTNLGEKLIDEEVDEMMTEADIDGDRQVD

Parental  YEEFVQMMTAK
          YEE..QMMTAK
Retrocopy YEELIQMMTAK

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	742.64 RPM
bodymap2_adrenal	0.00 RPM	520.27 RPM
bodymap2_brain	0.00 RPM	3148.45 RPM
bodymap2_breast	0.00 RPM	829.54 RPM
bodymap2_colon	0.00 RPM	1184.51 RPM
bodymap2_heart	0.00 RPM	480.06 RPM
bodymap2_kidney	0.00 RPM	470.27 RPM
bodymap2_liver	0.00 RPM	177.37 RPM
bodymap2_lung	0.00 RPM	721.85 RPM
bodymap2_lymph_node	0.00 RPM	451.49 RPM
bodymap2_ovary	0.00 RPM	480.03 RPM
bodymap2_prostate	0.00 RPM	796.81 RPM
bodymap2_skeletal_muscle	0.00 RPM	671.11 RPM
bodymap2_testis	0.00 RPM	554.04 RPM
bodymap2_thyroid	0.00 RPM	376.15 RPM
bodymap2_white_blood_cells	0.00 RPM	712.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3847 was not detected

EST

No EST(s) were mapped for retro_hsap_3847 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_176349	1338 libraries	426 libraries	61 libraries	3 libraries	1 library

The graphical summary, for retro_hsap_3847 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_3847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3847 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2623

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Parental genes homology:

Parental genes homology involve 33 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000001801	4 retrocopies	retro_amel_1215, retro_amel_1714, retro_amel_265, retro_amel_811,
Callithrix jacchus	ENSCJAG00000017740	3 retrocopies	retro_cjac_1418, retro_cjac_2564, retro_cjac_693,
Dasypus novemcinctus	ENSDNOG00000004645	9 retrocopies	retro_dnov_1093, retro_dnov_18, retro_dnov_1864, retro_dnov_1972, retro_dnov_2229, retro_dnov_241, retro_dnov_2522, retro_dnov_2674, retro_dnov_865,
Dipodomys ordii	ENSDORG00000003200	6 retrocopies	retro_dord_108, retro_dord_113, retro_dord_201, retro_dord_212, retro_dord_29, retro_dord_5,
Equus caballus	ENSECAG00000009162	1 retrocopy	retro_ecab_279,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Homo sapiens	ENSG00000160014	3 retrocopies	retro_hsap_1255, retro_hsap_1785, retro_hsap_59,
Homo sapiens	ENSG00000198668	2 retrocopies	retro_hsap_1290, retro_hsap_3847 ,
Gallus gallus	ENSGALG00000026445	1 retrocopy	retro_ggal_9,
Gorilla gorilla	ENSGGOG00000028540	1 retrocopy	retro_ggor_2592,
Gadus morhua	ENSGMOG00000009342	1 retrocopy	retro_gmor_23,
Latimeria chalumnae	ENSLACG00000005059	1 retrocopy	retro_lcha_53,
Loxodonta africana	ENSLAFG00000002905	1 retrocopy	retro_lafr_1165,
Meleagris gallopavo	ENSMGAG00000013055	1 retrocopy	retro_mgal_13,
Microcebus murinus	ENSMICG00000004980	3 retrocopies	retro_mmur_314, retro_mmur_35, retro_mmur_45,
Monodelphis domestica	ENSMODG00000002696	4 retrocopies	retro_mdom_137, retro_mdom_178, retro_mdom_185, retro_mdom_208,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000008087	1 retrocopy	retro_mputfur_523,
Mus musculus	ENSMUSG00000001175	4 retrocopies	retro_mmus_1519, retro_mmus_2859, retro_mmus_2871, retro_mmus_50,
Nomascus leucogenys	ENSNLEG00000017040	3 retrocopies	retro_nleu_2039, retro_nleu_2093, retro_nleu_2648,
Ornithorhynchus anatinus	ENSOANG00000015365	1 retrocopy	retro_oana_9,
Oryctolagus cuniculus	ENSOCUG00000011659	1 retrocopy	retro_ocun_626,
Otolemur garnettii	ENSOGAG00000028089	1 retrocopy	retro_ogar_1727,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000006060	1 retrocopy	retro_pabe_1045,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Pan troglodytes	ENSPTRG00000006626	1 retrocopy	retro_ptro_3043,
Pteropus vampyrus	ENSPVAG00000010028	1 retrocopy	retro_pvam_1274,
Rattus norvegicus	ENSRNOG00000004060	3 retrocopies	retro_rnor_318, retro_rnor_389, retro_rnor_392,
Sus scrofa	ENSSSCG00000025768	3 retrocopies	retro_sscr_26, retro_sscr_390, retro_sscr_692,
Tursiops truncatus	ENSTTRG00000013584	2 retrocopies	retro_ttru_1637, retro_ttru_1699,
Vicugna pacos	ENSVPAG00000004563	1 retrocopy	retro_vpac_472,