RetrogeneDB ID: retro_pabe_1045

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:41137168..41137613(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALM3
• Ensembl ID: ENSPPYG00000006060
• Aliases: None
• Description: Calmodulin [Source:UniProtKB/Swiss-Prot;Acc:Q5RAD2]

Sequence

>retro_pabe_1045
ATGGCTGACCAACTGACTGAAAGGCAGATTGCAGAATTCAAAGAAGCTTTTTCACTATTTGACAAAGATGGTGATGGAAC
TGTAACAACAAGGAATCAGGAACTGTAATGAGGTCTCTTGGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAA
TGAAGTAGATGCTGATGGTAATGGCACAGTTGACTTCCCTAATTTCTGACAATGAAGGCAAGAAAAATGAAAGACACAGA
CAGTGAAAAAGAAATTAGAGATGCATTCAGTGTGTTCAATAAGGATGGCAATGGCTATATTAGTGCAACAGAACTTCACC
ATGTGATGACAAGCCTTGGAGAGAATTTAACAGATGACGAGGTCGATGAAATGATCAGGTAATCAGATATTGATGGTGAA
GGTCAAATGATCTATGAAGAGTTTGTACAAATGATGACGGCAAAG

Alignment

ORF - retro_pabe_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADQLTEEQIAEFKEAFSLFDKDGDGTITT-KELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEF
          MADQLTE.QIAEFKEAFSLFDKDGDGT.TT.KE.GTVMRSLGQNPTEAELQDMINEVDADGNGT.DFP.F
Retrocopy MADQLTERQIAEFKEAFSLFDKDGDGTVTT<KESGTVMRSLGQNPTEAELQDMINEVDADGNGTVDFPNF

Parental  -LTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVN
          .LTM.ARKMKDTDSE.EIR.AF.VF.KDGNGYISA.EL.HVMT.LGE.LTD.EVDEMIR..DIDG.GQ..
Retrocopy <LTMKARKMKDTDSEKEIRDAFSVFNKDGNGYISATELHHVMTSLGENLTDDEVDEMIR*SDIDGEGQMI

Parental  YEEFVQMMTAK
          YEEFVQMMTAK
Retrocopy YEEFVQMMTAK

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
SRP007412_brain_prefrontal_cortex	0.33 RPM	3056.30 RPM
SRP007412_cerebellum	0.00 RPM	1727.83 RPM
SRP007412_heart	0.12 RPM	185.71 RPM
SRP007412_kidney	0.20 RPM	253.61 RPM
SRP007412_liver	0.06 RPM	135.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1045 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1045 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1255
Pan troglodytes	retro_ptro_3043
Gorilla gorilla	retro_ggor_988

---

Parental genes homology:

Parental genes homology involve 34 parental genes, and 79 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	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 ,
Pongo abelii	ENSPPYG00000010154	4 retrocopies	retro_pabe_1106, retro_pabe_1466, retro_pabe_3238, retro_pabe_3676,
Pongo abelii	ENSPPYG00000012430	5 retrocopies	retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
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,