RetrogeneDB ID: retro_sscr_26

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:117991435..117991885(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009126
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CALM1
• Ensembl ID: ENSSSCG00000025768
• Aliases: None
• Description: Sus scrofa calmodulin 1 (CALM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001244210]

Sequence

>retro_sscr_26
GTGGCTGACCAACTGACTGAAGAGCAGATTGCAGAAGTCCAAGAAGCTTTTTCACTATTTGACAAGGATGGTGATGGAAC
TATAACAACAAAGAAATTGGGAACTGTAATAAGGTCTCTTGGGCAGAATCCCACAGAAGCAGAGTTACAGGGCATGATTA
ATGAAGGAGAAGCTCATGGTAACGGCACAACTGACTTCCTGGAATTTCTGACAATGATGGCAGGAAAAATAAAAGACACA
GACAGTGAAGAAGAAATTAGAGAAGTATTCTGTGTGTTGGATAAGGATGGCAATGGCTATATTAGTGCCGGGGAGCTTCG
CCATGTGATGACAAACCTTGGAGACAAGTTAGCAGATGAAGAGGTTGATGAAATGATCAGGGAAGCAGATATTGATGGTG
ATGGTCAGGTAAACTATGAAGAGTTTGTACAAATGTTGACAGCAAAGTGA

Alignment

ORF - retro_sscr_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
          .ADQLTEEQIAE..EAFSLFDKDGDGTITTK.LGTV.RSLGQNPTEAELQ.MINE..A.GNGT.DF.EFL
Retrocopy VADQLTEEQIAEVQEAFSLFDKDGDGTITTKKLGTVIRSLGQNPTEAELQGMINEGEAHGNGTTDFLEFL

Parental  TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
          TMMA.K.KDTDSEEEIRE.F.V.DKDGNGYISA.ELRHVMTNLG.KL.DEEVDEMIREADIDGDGQVNYE
Retrocopy TMMAGKIKDTDSEEEIREVFCVLDKDGNGYISAGELRHVMTNLGDKLADEEVDEMIREADIDGDGQVNYE

Parental  EFVQMMTAK
          EFVQM.TAK
Retrocopy EFVQMLTAK

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
SRP014902_placenta	0.00 RPM	171.22 RPM
SRP014902_testis	0.00 RPM	72.42 RPM
SRP018288_heart	0.03 RPM	173.43 RPM
SRP018288_kidney	0.00 RPM	139.39 RPM
SRP018288_liver	0.16 RPM	56.93 RPM
SRP018288_lung	0.00 RPM	192.45 RPM
SRP018856_adipose	0.02 RPM	205.37 RPM
SRP035408_brain	0.48 RPM	1287.25 RPM
SRP035408_liver	0.00 RPM	60.06 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_26 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_26 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 69 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,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Pan troglodytes	ENSPTRG00000006626	1 retrocopy	retro_ptro_3043,
Rattus norvegicus	ENSRNOG00000004060	3 retrocopies	retro_rnor_318, retro_rnor_389, retro_rnor_392,
Sus scrofa	ENSSSCG00000008433	1 retrocopy	retro_sscr_228,
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,