RetrogeneDB ID: retro_sscr_593

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:15523186..15524351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016538
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSSSCG00000007088
• Aliases: None
• Description: sorting nexin 5 [Source:HGNC Symbol;Acc:14969]

Sequence

>retro_sscr_593
AAGCTACGATCTGTATCAGTGGACCTGAATGTTGATCCTTCACTTCAGATCGACATACCTGATGCACTCAGTGAGAGAGA
TAAAATCAAATTTACAGTACACACCAAGACCACGCTGCCCACGTTTCAGAGTCCAGAGTTTTCTGTTACGAGGCAACATG
AAGACTTTGTGTGGCTACATGACACTCTTATTGAAACTACAGACTATGCTGGGCTTATTATTCCACCTGCACCTACGAAG
CCTGACTTTGATGGGCCTCGAGAAAAGATGCCAAAACTGGGAGACGGTGAAGGGTCAATGACCAAAGAAGAATTTGCCAA
GATGAAGCAAGAGCTGGAAGCTGAGTATCTTGCTGTCTTTAAGAAGACTCTGTCCTCTCATGAGGTCTTTCTTCAGCGGC
TCTCCTCTCATCCTGTTCTCAGTAAAGATCGAAACTTTCATTTTTTCCTGGAATATGACCAAGATCGAAGTGTTAGGAGG
AAAAAATACCAAAGAGATGTTCACTGGCTTTTTCAAAAGTGTGGTGAAAAGTGCTGATGAAATCCTTTTTTTCAGGAGTT
AAGGAGGTAGATGATTTCTTTGAGCAAGAGAAGAATTTCCTCATTAACTGCTATAATAAGATCAAGGATTCATGTGCAAA
GGCTGACAGAATGACCAGATCTCATAAAAATGTTGTTGACAACTACGTCCACACTGCAGCTTGCCTGCATAGTCTCGCTT
CAGAAGAGCCCATGGTCATCAAAAAGTACCTATTGAAGGTTGCTAAGCTATTTGAAAAACTTAGGAAAGTAGAGAGTCGG
GTCTCCTCGGATGAAGACTTGAAGCTGCCAGAGCTTCTCCGGTACTACATGCTCGACATTGAGGCCGCTAAGATCTCTTA
TACAGACGCACCAAAGCCCTCATTGACTGTGGGAATTCAAACAAAGCATTGGATAAGGCCCGGTTAAAAAGCAGAGACAT
CCAGTTGGCTGAGGCACACCAGCAAGAATGCTGCCAGAAATTGGAACAGCTTTCTGAATCTGCAAAAGAAGAGCTGATCA
ATTTCACATGATAGAGAGTGGCGGCATTTAGAAAGAATCTAATCGAAATGTCAGAACTGCAAATAAAGCATGCCAGGAAC
AATGCCTCCCTTCTGCAGAGCTGCATTGACTTGTTCAAGAACAAC

Alignment

ORF - retro_sscr_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 93.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYA
          .LRSVSVDLNVDPSLQIDIPDALSERDK.KFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYA
Retrocopy KLRSVSVDLNVDPSLQIDIPDALSERDKIKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYA

Parental  GLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHPVL
          GLIIPPAPTKPDFDGPREKM.KLG.GEGSMTKEEFAKMKQELEAEYLAVFKKT.SSHEVFLQRLSSHPVL
Retrocopy GLIIPPAPTKPDFDGPREKMPKLGDGEGSMTKEEFAKMKQELEAEYLAVFKKTLSSHEVFLQRLSSHPVL

Parental  SKDRNFHVFLEYDQDLSVRR-KNTKEMFGGFFKSVVKSADEVL-FSGVKEVDDFFEQEKNFLINYYNRIK
          SKDRNFH.FLEYDQD.SVRR.KNTKEMF.GFFKSVVKSADE.L.FSGVKEVDDFFEQEKNFLIN.YN.IK
Retrocopy SKDRNFHFFLEYDQDRSVRR>KNTKEMFTGFFKSVVKSADEIL>FSGVKEVDDFFEQEKNFLINCYNKIK

Parental  DSCAKADRMTRSHKNVADDYIHTAACLHSLASEEPTVIKKYLLKVAELFEKLRKVESRVSSDEDLKLTEL
          DSCAKADRMTRSHKNV.D.Y.HTAACLHSLASEEP.VIKKYLLKVA.LFEKLRKVESRVSSDEDLKL.EL
Retrocopy DSCAKADRMTRSHKNVVDNYVHTAACLHSLASEEPMVIKKYLLKVAKLFEKLRKVESRVSSDEDLKLPEL

Parental  LRYYMLNIEAAK-DLLYRRTKALIDYENSNKALDKARLKSRDIKLAEAHQQECCQKFEQLSESAKEVELI
          LRYYML.IEAAK.DLLYRRTKALID..NSNKALDKARLKSRDI.LAEAHQQECCQK.EQLSESAKE.ELI
Retrocopy LRYYMLDIEAAK<DLLYRRTKALIDCGNSNKALDKARLKSRDIQLAEAHQQECCQKLEQLSESAKE-ELI

Parental  NFKRKRVAAFRKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
          NF...RVAAFRKNLIEMSEL.IKHARNN.SLLQSCIDLFKNN
Retrocopy NFT**RVAAFRKNLIEMSELQIKHARNNASLLQSCIDLFKNN

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	0.27 RPM	43.14 RPM
SRP014902_testis	0.42 RPM	106.51 RPM
SRP018288_heart	0.21 RPM	47.86 RPM
SRP018288_kidney	0.59 RPM	213.46 RPM
SRP018288_liver	0.48 RPM	99.94 RPM
SRP018288_lung	0.00 RPM	49.28 RPM
SRP018856_adipose	0.21 RPM	68.30 RPM
SRP035408_brain	0.00 RPM	53.10 RPM
SRP035408_liver	0.06 RPM	122.65 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_593 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_593 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593 ,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,