RetrogeneDB ID: retro_pcap_65

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3702:19385..20258(+)
• Located in intron of: ENSPCAG00000005059

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35B3
• Ensembl ID: ENSPCAG00000006201
• Aliases: None
• Description: solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3 [Source:HGNC Symbol;Acc:21601]

Sequence

>retro_pcap_65
ATAATATTTTCAGTGGAGGTCTTTAAGTCCTATGGCTGGTACCTTGTATTAGTACCGTTTGGGTTTTACTCTATCTGGCC
CAACAGAACTTCAGCTTATTCAGGACAAATGGAGTCTACCAGGAAAACCTACATGATAATAGCTTTCTATCCATTGGGTA
CTATGGGGTTACCAGACATTTCTTTGGATGATCTGAATTACTGTACCCAAATCATCTTCAAGCATTGCACACTGATTTCT
GTTATGCTGGGAGGAGTTTTTTTCCAAGGAAAGCAATAGGACATTACAGATACGTCTGCTGCAGCATAGATGAGCCTTGG
CCTGATGTGGTTTAACCCAGCTGACAGCACTGTTGCTCCAAATTTCACCCCGATAGGGGTGATCCTTCTTATCTCACTGG
CACTGTGTGCAGATGGTGTTGCTAGAACTATCCAAGAGAAAGCTAGGAAACTGCATGATGCTTCTAATTAAGAAACGCGT
CTGAATTTGTATTCTGTAGGTTTTGTGTTCATTTTATCAGGGTGTGCACTTGTGGATTGTGCCCTGCAATAACGTTTTGT
TCAAAGAACCCAATTTGGACCTGCAGTTATGCTGTTTTTTCCCCCTCACTGAGTAGGTTGAAATCTTCTTTGTTCTGGCT
TTGTTTGAAAATTTGGACCACTTCTTGCTGTAACAGTGACAACAGGAAGAAAAGCCATGACTGCTGAGCTTTCATTTATG
TTTTTTGCTAAACCAGTCACATGTCAGTATGTCTGGTCTGATCTGTTAGTTGTTCTTGGTCTGTTTCTCAGTGTTTAGAG
CAAAAATACGGACAAAATAAGACTACCATCATTACAAGATAAATCAGTGGGTGAGAAAAAGTCAGAAATGTTG

Alignment

ORF - retro_pcap_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LIFSVEGFKPYGWYLTLVQF-GFYSIFGLIELQLIQDKRRRIPGQ-TYMIIAFLTVGTMGLSNTSLGYLN
          .IFSVE.FK.YGWYL.LV.F.GF....G..ELQLIQDK....PG..TYMIIAF...GTMGL...SL..LN
Retrocopy IIFSVEVFKSYGWYLVLVPF>GF-TLSGPTELQLIQDKWS-LPGK<TYMIIAFYPLGTMGLPDISLDDLN

Parental  YPTQVIFKCCKLIPVMLGGVFIQGKRYNIADVSAAVCMSLGLIWFTLADSTVAPNFNLTGVVL-ISLALC
          Y.TQ.IFK.C.LI.VMLGGVF.QGK...I.D.SAA..MSLGL.WF..ADSTVAPNF...GV.L.ISLALC
Retrocopy YCTQIIFKHCTLISVMLGGVFFQGKQ*DITDTSAAA*MSLGLMWFNPADSTVAPNFTPIGVILLISLALC

Parental  ADAVIGNVQEKAMKLHNASNSEMVLYSYSIG-FVYIFLGLTCTSGLRPAVAFCSKNPVRTYGYAFL-FSL
          AD.V....QEKA.KLH.ASN.E..L..YS.G.F...F....CT.GL.PA..FCSKNP..T..YA...F.L
Retrocopy ADGVARTIQEKARKLHDASN*ETRLNLYSVG<FCVHFIRV-CTCGLCPAITFCSKNPIWTCSYAVF<FPL

Parental  TGYFGISFVLALIKI-FGALLAVTVTTGRKAMTIILSFLFFAKPFTFQYVWSGLLVVLGIFLNVYSKNMD
          T....I.FVLAL....FG.LLAVTVTTGRKAMT..LSF.FFAKP.T.QYVWS.LLVVLG.FL.V.SKN.D
Retrocopy TE*VEIFFVLALFEN<FGPLLAVTVTTGRKAMTAELSFMFFAKPVTCQYVWSDLLVVLGLFLSV*SKNTD

Parental  KIRLPSLQGLINRWVDERKSRTL
          KIRLPSLQ......V.E.KS..L
Retrocopy KIRLPSLQ---DKSVGEKKSEML

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_65 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002579	1 retrocopy	retro_lafr_641,
Procavia capensis	ENSPCAG00000006201	1 retrocopy	retro_pcap_65 ,