RetrogeneDB ID: retro_cpor_277

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_113:949590..950817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC30A5
• Ensembl ID: ENSCPOG00000003972
• Aliases: None
• Description: None

Sequence

>retro_cpor_277
TCCTTTCCCATGTTTATTAGTGCTCTCCTTTTTAGAAATTTTTGGACATGCCCAATAACAGTCCAGCTTCAGGCTATGAA
CAGAGCTACACACCAGGAGGGCGTGGAGAACATCCTGTTTGGAGGAATGATCCTCAGTGCTGTGTTCTTCGCTTTGTCTG
TCAACATTTTATCATTTTGCTCTACAAAGGAGAGAGAGGTACCCTTATTGGGTTTTCTCCTGAAGGAACACCTCTTTATA
ACTTCATGGATGATGCTTTCAGCACAACTCTCAATCAACCACTAGGTTTAATAAGGAATCACCAAAACAAATTCTTGAAG
CGAGTGACTCTAGGCAGATCTTTTACTTCCTGTGCTTGAATCTGCTCTTTACCTTGGTGGAATTCTTCTATACTGTGTCG
ACCAATAGTCTGAGTCTGATCTCAGATAGATTTCAGATGCTCTTTGATTACCCTGCTTGGATCATGGGACTTTTTGCTGT
TCTGATGAATAGATGGAAAGCTACTCCAATTTTCTCCTATGGGTATGGTCAAGTAGAAATTCTCTCTGGATTGATTAATG
TACTTTTCTAATAATAATAGATTTTTGTGTTTATGGATCAGTTACTAGATTGATTGACCCTTCAGAATTAGGCAAGAACA
TGTTGACACCAGTCTAAGTTGGAGAACTGACCATAAACCTTATTGCTATTTGTGCCTTTAGCCATGTCCATAGCCACAAC
CATGGAACTTCACAAAGAAGCTGTCACTCATCTGATCACAGCCACTCACATCAAACACATGGACATAGTGACCATGGGCA
TGGTCAGAGCCACAGACCCCAAGGCAGAGGCATTAGTGCCAACAATGAGGGGTGTATTTCTGCATGTTTTCACAGACACA
CTTGGCAGTATTTGTATGATTGTTTCTACAGTTCTGACAGAGCAGTTTAGGTGGTTCTTTGCCAATTCCTCTGTTCACTT
TTTATTGTTGTGTTTTTAGTTCTCAGTGTTGTCTGTCCCACTGATTGAAGATGCCTGTCAAGTTCTGCATCTAAGGCTGC
TACAAGAACATGAGAAAATAAATAGACTGCTTGAGAAAATATACATAAAATGGAAGGATTAATATCATATCAATACCCTT
ATTTTTGGCATAATTCTACCAGTATTATAACAAGAACAATTCATATACAGGTAACACCTGATGTGCTAGAACAAAGAATA
GTACAGTAGATTACAGGAATACTGGAG

Alignment

ORF - retro_cpor_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.57 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SFPIFISALLFGNFWTHPITDQLRAMNRATHQESTEHVLSGGVVVSAVFFILSANILSSPSKR-GQKGTL
          SFP.FISALLF.NFWT.PIT.QL.AMNRATHQE..E..L.GG...SAVFF.LS.NILS..S...G..GTL
Retrocopy SFPMFISALLFRNFWTCPITVQLQAMNRATHQEGVENILFGGMILSAVFFALSVNILSFCSTK<GERGTL

Parental  IGYSPEGTPLYNFMGDAF-QHSSQSIPRFIKESLKQILEESDSRQIFYFLCLNLLFTFVELFYGVLTNSL
          IG.SPEGTPLYNFM.DAF.QH.SQS..RF.KES.KQILE.SDSRQIFYFLCLNLLFT.VE.FY.V.TNSL
Retrocopy IGFSPEGTPLYNFMDDAF<QHNSQSTTRFNKESPKQILEASDSRQIFYFLCLNLLFTLVEFFYTVSTNSL

Parental  GLISDGFHMLFDCSALVMGLFAALMSRWKATRIFSYGYGRIEILSGFINGLF-LIVIAFFVFMESVARLI
          .LISD.F.MLFD..A..MGLFA.LM.RWKAT.IFSYGYG..EILSG.IN.LF.LI.I.F.V...SV.RLI
Retrocopy SLISDRFQMLFDYPAWIMGLFAVLMNRWKATPIFSYGYGQVEILSGLINVLF<LIIIDFCVY-GSVTRLI

Parental  DPPELDTNMLTPVSVGGLIVNLIGICAFSHAHSHSHGTSQGGCHSSDHSHSHHTHGHSDHGHSHSHGPSG
          DP.EL..NMLTPV.VG.L..NLI.ICAFSH.HSH.HGTSQ..CHSSDHSHSH.THGHSDHGH..SH.P.G
Retrocopy DPSELGKNMLTPV*VGELTINLIAICAFSHVHSHNHGTSQRSCHSSDHSHSHQTHGHSDHGHGQSHRPQG

Parental  GGMNAN-MRGVFLHVLADTLGSIGVIVSTVLIEQFGWFVADP-LCSLF-IAVLIFLSV-VPLIKDACQVL
          .G..AN.MRGVFLHV..DTLGSI..IVSTVL.EQF.WF.A...LCSLF....L....V.VPLI.DACQVL
Retrocopy RGISAN>MRGVFLHVFTDTLGSICMIVSTVLTEQFRWFFANS<LCSLFIVVFLVLSVV>VPLIEDACQVL

Parental  LLRLPPEHE-KELHTALEKIQKIEGLISYRDPHFWRHSASIVAGTIHIQVTSDVLEQRIVQQVTGILK
          .LRL..EHE.....TA.E.I.K.EGLISY..P.FW..S.SI...TIHIQVT.DVLEQRIVQ..TGIL.
Retrocopy HLRLLQEHE<ENK*TA*ENIHKMEGLISYQYPYFWHNSTSIITRTIHIQVTPDVLEQRIVQ*ITGILE

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
SRP017611_brain	0.00 RPM	32.50 RPM
SRP017611_kidney	0.00 RPM	57.37 RPM
SRP017611_liver	0.00 RPM	46.44 RPM
SRP040447_lung	0.00 RPM	55.33 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_277 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_277 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003972	1 retrocopy	retro_cpor_277 ,