RetrogeneDB ID: retro_pabe_1466

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:60042879..60043347(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALM3
• Ensembl ID: ENSPPYG00000010154
• Aliases: None
• Description: calmodulin 3 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1449]

Sequence

>retro_pabe_1466
AAACCGGTAGGAGTTGCAGCATGGCAGACCAAACTGACTGAAGAGCAGATTCCAGAATTCATGGAAGCTTTTTCACTATT
TGACAGAGACGATGATGGAACTATAACAACAAAGGAATTGGAAACGATCATGAGGTCTCTTGGGTAGAATCCCACGAAAG
CAGGGTTACTAGACATGATTAATGAAGTAGATGCTGATGGTAATAGAACAACGGACCCTCCTGAATTTCTGACAATGATG
GCAAGAAAAATGAAAGACACACAAAGTGAAGAAGAAATTAGAGAAGCATTCCTTGTGTTTGATAAGGATGGCAATGGCTA
TATCAGCACAGCAGAACTTCGCCATGTGATGACAAACCCTGGAGAGAAGCTAACAGATGACAAGGTTGATTAAATCATCA
GGGAAGCAGGTATTGATGATGATGGTCAAGTAAACTAGGAAGAGTTTGTACAAATGATGACAGCAAAG

Alignment

ORF - retro_pabe_1466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPVPGLASADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGT
          KPV...A....LTEEQI.EF.EAFSLFD.D.DGTITTKEL.T.MRSLG.NPT.A.L.DMINEVDADGN.T
Retrocopy KPVGVAAWQTKLTEEQIPEFMEAFSLFDRDDDGTITTKELETIMRSLG*NPTKAGLLDMINEVDADGNRT

Parental  IDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDG
          .D.PEFLTMMARKMKDT.SEEEIREAF.VFDKDGNGYIS.AELRHVMTN.GEKLTD..VD..IREA.ID.
Retrocopy TDPPEFLTMMARKMKDTQSEEEIREAFLVFDKDGNGYISTAELRHVMTNPGEKLTDDKVD*IIREAGIDD

Parental  DGQVNYEEFVQMMTAK
          DGQVN.EEFVQMMTAK
Retrocopy DGQVN*EEFVQMMTAK

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	0.06 RPM	3192.98 RPM
SRP007412_cerebellum	0.00 RPM	631.35 RPM
SRP007412_heart	0.00 RPM	201.24 RPM
SRP007412_kidney	0.00 RPM	296.73 RPM
SRP007412_liver	0.00 RPM	104.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1466 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1466 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1785
Pan troglodytes	retro_ptro_1195
Gorilla gorilla	retro_ggor_2234
Callithrix jacchus	retro_cjac_2564

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000008565	3 retrocopies	retro_amel_1209, retro_amel_1562, retro_amel_421,
Bos taurus	ENSBTAG00000014583	2 retrocopies	retro_btau_113, retro_btau_135,
Canis familiaris	ENSCAFG00000029151	4 retrocopies	retro_cfam_121, retro_cfam_164, retro_cfam_225, retro_cfam_68,
Cavia porcellus	ENSCPOG00000001612	1 retrocopy	retro_cpor_1316,
Erinaceus europaeus	ENSEEUG00000000140	1 retrocopy	retro_eeur_468,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Felis catus	ENSFCAG00000004995	1 retrocopy	retro_fcat_1726,
Homo sapiens	ENSG00000160014	3 retrocopies	retro_hsap_1255, retro_hsap_1785, retro_hsap_59,
Gorilla gorilla	ENSGGOG00000000212	4 retrocopies	retro_ggor_187, retro_ggor_2234, retro_ggor_522, retro_ggor_988,
Loxodonta africana	ENSLAFG00000001155	5 retrocopies	retro_lafr_100, retro_lafr_156, retro_lafr_631, retro_lafr_646, retro_lafr_86,
Microcebus murinus	ENSMICG00000013180	3 retrocopies	retro_mmur_1032, retro_mmur_1447, retro_mmur_501,
Myotis lucifugus	ENSMLUG00000010528	1 retrocopy	retro_mluc_2477,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000005261	1 retrocopy	retro_mputfur_404,
Mus musculus	ENSMUSG00000019370	3 retrocopies	retro_mmus_2879, retro_mmus_3448, retro_mmus_454,
Nomascus leucogenys	ENSNLEG00000002752	2 retrocopies	retro_nleu_1407, retro_nleu_3097,
Otolemur garnettii	ENSOGAG00000014764	2 retrocopies	retro_ogar_2085, retro_ogar_3311,
Procavia capensis	ENSPCAG00000005751	1 retrocopy	retro_pcap_7,
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,
Ictidomys tridecemlineatus	ENSSTOG00000014352	1 retrocopy	retro_itri_1018,