RetrogeneDB ID: retro_sscr_326

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:103956914..103958524(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC30A9
• Ensembl ID: ENSSSCG00000008801
• Aliases: None
• Description: Sus scrofa solute carrier family 30 (zinc transporter), member 9 (SLC30A9), mRNA. [Source:RefSeq mRNA;Acc:NM_001137632]

Sequence

>retro_sscr_326
GCCTGCGGCTCCAGCGACCGCCAGGAATGGCAGAATTTAGTGCCATTTGGAAGCTTTTCAAACATTGTTCCCTGTTGCAC
GCTGAATCAAGTAAAGTTGTACTCCACAAATGTTCAGAAAGAAGGACAGGGATCACCAACTCTCAAAATGGAAAAAGTAC
CATCATTTGATGAAACTGCAGAAAATATTGGTGCAGAACTGAAAGCTCCACTTCTTAAGAAAGAACCTCTCCAAGTAAGA
GTCAAAGCAGTCCTTAAAAAGAGGGAATATGGACCAAAATACACTCAGAATAATTTCATCACTGGAGTCAGAGCAATGAA
TGAGTTCTGCCTCAAATCCAGCGATCTAGAACAGCTTGGAAAAATCAGACGATGAAGTCCTCATGAAGATACTGAGTCCT
TTACTGTATACTTGAGATCAGATGTGGAGGCAAAATCTTTGGAAGTTTGGGGAAGCCCTGAAGCTCTTGCCAGAGAGAAA
AAACTTCATAAAGAAGCAGAAATAGAATATAGAGAAAGGTTATTTCGAAACCAAAAAATATTGAGAGAATACAGAGACTT
TCTGGGAAATACTAAGCCACGCTCTCGAGAGACATCAATTTTTTTTAGGGGGCCAGGAAAAGTGGTGATTGTTGCCATTT
GCATCAATGGATTAAACTGCTTCTTCAAATTTCTTGCCTGGATTTATACAGGTTCAGCAAGTATGTTCTCAGAAGCTGTA
TATTCTTTATCTGATACTTGTAATCAGGGCTTACTAGCATTGGGCATCAGAAAGTCTGTTCAAACACCAGATCCTACTCA
TCCGTATGGATTTTCGAATATGCGCTATATTGCTTCACTAATTAGTGGTGTTGGTATTTTCATGATGGGTGCAGGATTAT
CTTGGTATTATGGAATCATGGGATTGCTTGATCCTCAACCAATAGAATCTCTTCTATGGGCATATTGTATTTTAGCGGGA
TCATTGGTATCTGAAGGAGCAAAACTTCTTGTTGCTATAAATGAGCTTCATAGGAGTGCTCGGGCCAAAGGAATGTCATT
TTACAAGTATGTAATGGAAAGTTGTGATCCTAGTACGAATGTTATTTTATTGGAGGATACTGCAGCAGTGTTGGGAGTGA
TAATAGCCGCCACTTGTATGGGCCTTACTTCTGTAACAGGCAACCCACTGAATGACAGCCTAGGTTCTTTGGGTGTGGGC
ACATTATTAGGCGTCGTCTCAGTATTCCTCATCTACACTAGCACAGAAGCCCTCTTAGGGCGATCCATCCAGCCAGACCA
AGTATAGCAGCTTACTGAACTTCTGGAGAACAACCCATCAGTAAGGGCAATTCATGATGTTAAAGCCACAGATCTGGGAT
TAGGGAAAGTAAGATTTAAGGAGGAAGTAGATTTTGATGGACAAGTTGTTACAAGATCATATTTGGAAAAACAAGATTTG
ACCAGATGCTACAAGAAATTCAAGAAGTGAAAACTCCTGAAGAACTAGAGACCTTTATGCTTAAACATGGAGAAAATATT
ATTGATACTTTAGGAGCTGAAGTAGACAGACTTGAGAAGGAACAGAAAAAACAAAATCCTGAAGTTCGACATGTAGATCT
GGAAATACTA

Alignment

ORF - retro_sscr_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.24 %
• Parental protein coverage: 94.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARGSSDRQEWQNLVSFGSFSNIVPCCTLNQVKLYSTNVQKEGQGSQTLKMEKVPSFDETAENIGAELKAP
          A.GSSDRQEWQNLV.FGSFSNIVPCCTLNQVKLYSTNVQKEGQGS.TLKMEKVPSFDETAENIGAELKAP
Retrocopy ACGSSDRQEWQNLVPFGSFSNIVPCCTLNQVKLYSTNVQKEGQGSPTLKMEKVPSFDETAENIGAELKAP

Parental  LLKQEPLQVRVKAVLKKREYGPKYTQNNFITGVRAMNEFCLKSSDLEQLRKIRRRSPHEDTESFTVYLRS
          LLK.EPLQVRVKAVLKKREYGPKYTQNNFITGVRAMNEFCLKSSDLEQL.KIRR.SPHEDTESFTVYLRS
Retrocopy LLKKEPLQVRVKAVLKKREYGPKYTQNNFITGVRAMNEFCLKSSDLEQLGKIRR*SPHEDTESFTVYLRS

Parental  DVEAKSLEVWGSPEALAREKKLRKEAEIEYRERLFRNQKILREYRDFLGNTKPRSRATSIFFKGPGKVVI
          DVEAKSLEVWGSPEALAREKKL.KEAEIEYRERLFRNQKILREYRDFLGNTKPRSR.TS....GPGKVVI
Retrocopy DVEAKSLEVWGSPEALAREKKLHKEAEIEYRERLFRNQKILREYRDFLGNTKPRSRETSXXXRGPGKVVI

Parental  VAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTCNQGLLALGISKSVQTPDPTHPYGFSNMRYIASL
          VAICINGLNCFFKFLAWIYTGSASMFSEA..SLSDTCNQGLLALGI.KSVQTPDPTHPYGFSNMRYIASL
Retrocopy VAICINGLNCFFKFLAWIYTGSASMFSEAVYSLSDTCNQGLLALGIRKSVQTPDPTHPYGFSNMRYIASL

Parental  ISGVGIFMMGAGLSWYHGIMGLLNPQPIESLLWAYCILAGSLVSEGATLLVAINELRRSARAKGMSFYKY
          ISGVGIFMMGAGLSWY.GIMGLL.PQPIESLLWAYCILAGSLVSEGA.LLVAINEL.RSARAKGMSFYKY
Retrocopy ISGVGIFMMGAGLSWYYGIMGLLDPQPIESLLWAYCILAGSLVSEGAKLLVAINELHRSARAKGMSFYKY

Parental  VMESRDPSTNVILLEDTAAVLGVIIAATCMGLTSVTGNPLYDSLGSLGVGTLLGVVSAFLIYTNTEALLG
          VMES.DPSTNVILLEDTAAVLGVIIAATCMGLTSVTGNPL.DSLGSLGVGTLLGVVS.FLIYT.TEALLG
Retrocopy VMESCDPSTNVILLEDTAAVLGVIIAATCMGLTSVTGNPLNDSLGSLGVGTLLGVVSVFLIYTSTEALLG

Parental  RSIQPDQVQRLTELLENDPSVRAIHDVKATDLGLGKVRFKAEVDFDGRVVTRSYLEKQD-FDQMLQEIQE
          RSIQPDQV..LTELLEN.PSVRAIHDVKATDLGLGKVRFK.EVDFDG.VVTRSYLEKQD.FDQMLQEIQE
Retrocopy RSIQPDQV*QLTELLENNPSVRAIHDVKATDLGLGKVRFKEEVDFDGQVVTRSYLEKQD<FDQMLQEIQE

Parental  VKTPEELETFMLKHGENIIDTLGAEVDRLEKELKKRNPEVRHVDLEIL
          VKTPEELETFMLKHGENIIDTLGAEVDRLEKE.KK.NPEVRHVDLEIL
Retrocopy VKTPEELETFMLKHGENIIDTLGAEVDRLEKEQKKQNPEVRHVDLEIL

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	0.13 RPM	12.87 RPM
SRP014902_testis	0.00 RPM	22.35 RPM
SRP018288_heart	0.10 RPM	40.36 RPM
SRP018288_kidney	0.10 RPM	74.37 RPM
SRP018288_liver	0.00 RPM	15.51 RPM
SRP018288_lung	0.10 RPM	45.92 RPM
SRP018856_adipose	0.00 RPM	40.24 RPM
SRP035408_brain	0.03 RPM	41.42 RPM
SRP035408_liver	0.03 RPM	15.62 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_326 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_326 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326 ,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658,