RetrogeneDB ID: retro_sscr_73

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:27483085..27483826(-)
• Located in intron of: ENSSSCG00000002828

Retrocopy information

• Ensembl ID: ENSSSCG00000030744
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSSSCG00000030149
• Aliases: None
• Description: Sus scrofa calpain, small subunit 1 (CAPNS1), mRNA. [Source:RefSeq mRNA;Acc:NM_214318]

Sequence

>retro_sscr_73
ATGTTTCTTGCAAAGGCTCTCTTGGAAGGGGCAGATCAAGGTCTCGGACAAGCTCTTGGAGGCCTTCTTGGAGGTGGCGG
TCAGAGAAGAGGAGGAGGAAATATTGGAGGGATAGTTGGAGGAATTGTGAATTTTATCAGTGAGTCTGCAGCAGCTCAGT
ACACCCCGGAACCACCACCCACTCAGCAGCACTTCACCAACGTGGAGGCCAATGAAAGTGATGAAGTTAGGCGGTTTCGG
CAGCAATTCGCACAGCTGGCTGGACCAGACATGGAGGTGGGTGCCACTGACCTGATGAATATTCTCAACAAAGTCCTTTC
TAAGCACAAGGATCTGAAGTCTGACGGCTTTAGTCTTGACACCTGCCGGAGCATCGTGTCCGTTATGGACAGTGACACCA
CTGGGAAGCTGGGCTTCGAAGAATTTAAGTATCTCTGGAACAACATTAAGAAGTGGCAGTGCATTTATAAGCAATATGAC
AGGGACCAGTCCGGGTCTCTGGGAAGTTCTCAGGTGCGGGGGGCTCTGCAGGCAGCAGGCTTCCAGCTAAATGAACAACT
TTACCAAACGATTATCCGCCGATATGCAGAAGAGGATGGAAGAATGGATTTTAACAGCTTCATCAGCTGCCTGGTCCGCC
TGGATGCCATGTTTCGTGCCTTCAGATCCCTGGATAGAGATGCCGATGGCCTGATTCAGGTGTATATCCAAGAATGGCTT
CAGCTGACCATGTATTCCTGA

Alignment

ORF - retro_sscr_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 89.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLGGLISGAGGGGGGGGGGGGGGGGGGTAMRILGGVISAISE-AAAQYNPEPPPPRTHYSNIEANESEEV
          .L.G...G.G...GG..GGGG...GGG....I.GG....ISE.AAAQY.PEPPP...H..N.EANES.EV
Retrocopy LLEGADQGLGQALGGLLGGGGQRRGGGNIGGIVGGIVNFISESAAAQYTPEPPPTQQHFTNVEANESDEV

Parental  RQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLW
          R.FR..FAQLAG.DMEV.AT.LMNILNKV...H.DLK.DGF..DTCRS.V.VMDSDTTGKLGFEEFKYLW
Retrocopy RRFRQQFAQLAGPDMEVGATDLMNILNKVLSKHKDLKSDGFSLDTCRSIVSVMDSDTTGKLGFEEFKYLW

Parental  NNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDA
          NNIKKWQ.IYKQ.D.D.SG..GSS...GA..AAGF.LNE.LY..IIRRY..E.G.MDF..FISCLVRLDA
Retrocopy NNIKKWQCIYKQYDRDQSGSLGSSQVRGALQAAGFQLNEQLYQTIIRRYAEEDGRMDFNSFISCLVRLDA

Parental  MFRAFKSLDKDGTGQIQVNIQEWLQLTMYS
          MFRAF.SLD.D..G.IQV.IQEWLQLTMYS
Retrocopy MFRAFRSLDRDADGLIQVYIQEWLQLTMYS

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	1.06 RPM	1102.73 RPM
SRP014902_testis	0.71 RPM	267.19 RPM
SRP018288_heart	0.10 RPM	97.05 RPM
SRP018288_kidney	0.00 RPM	274.73 RPM
SRP018288_liver	0.00 RPM	130.81 RPM
SRP018288_lung	0.31 RPM	483.98 RPM
SRP018856_adipose	0.23 RPM	665.23 RPM
SRP035408_brain	0.32 RPM	108.37 RPM
SRP035408_liver	0.09 RPM	66.26 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_73 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_73 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_73 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_98
Pan troglodytes	retro_ptro_1112
Gorilla gorilla	retro_ggor_1241
Pongo abelii	retro_pabe_1359
Macaca mulatta	retro_mmul_1567
Mus musculus	retro_mmus_80
Rattus norvegicus	retro_rnor_1447
Bos taurus	retro_btau_692
Canis familiaris	retro_cfam_942
Equus caballus	retro_ecab_707

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940,
Cavia porcellus	ENSCPOG00000000115	1 retrocopy	retro_cpor_1131,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Echinops telfairi	ENSETEG00000007650	2 retrocopies	retro_etel_1190, retro_etel_60,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Gorilla gorilla	ENSGGOG00000003699	2 retrocopies	retro_ggor_1241, retro_ggor_263,
Microcebus murinus	ENSMICG00000010255	1 retrocopy	retro_mmur_416,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Nomascus leucogenys	ENSNLEG00000011712	2 retrocopies	retro_nleu_1328, retro_nleu_992,
Ornithorhynchus anatinus	ENSOANG00000002736	1 retrocopy	retro_oana_113,
Oryctolagus cuniculus	ENSOCUG00000013093	1 retrocopy	retro_ocun_1095,
Otolemur garnettii	ENSOGAG00000006992	1 retrocopy	retro_ogar_1956,
Ochotona princeps	ENSOPRG00000016562	2 retrocopies	retro_opri_181, retro_opri_486,
Procavia capensis	ENSPCAG00000006353	1 retrocopy	retro_pcap_165,
Pongo abelii	ENSPPYG00000009898	2 retrocopies	retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pan troglodytes	ENSPTRG00000010887	2 retrocopies	retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73 ,
Ictidomys tridecemlineatus	ENSSTOG00000026235	1 retrocopy	retro_itri_342,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,