RetrogeneDB ID: retro_pcap_346

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_44848:14350..15652(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX21
• Ensembl ID: ENSPCAG00000016697
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 21 [Source:HGNC Symbol;Acc:2744]

Sequence

>retro_pcap_346
AAGTTACTTGTATTGACTCCACCAAGGGAACTGACAAACCACATAGACAAAGACTTCAAAGAGGTAACCAGAAAACTCAG
TATGGCATGTTTTTTATGGTCGATCATCATATGAAAGCCAAACAAACCATATTTGAAATGATGTTGATGTCTTGCTTGGG
ACCCCAGTTGTATCAAACGACTGTGCGCAGAGTGGCCAATGGGATCTTTCTAAACTCTGTCATGTTATGCTTGAGGTGGA
TCAAATGGTAGATTTACGGTTTGCTGAACAAGTTGAAGATATTATCCCACAAACTCTACAGAACTAATCCCAAAGACAAT
CCTCAGACTTTACTTCTTTCTGCAACTTGCCCTCATGGATATACAAAGCTGTAAAAAAAAAAATACATGAAATCTGATAT
AAACAGGTTGACCTTGTTGGAAAAATAACTCATAAGGATGCAACTCCTGTGGAACACTTGGCCATCCAGTGCCATTGGTC
TCAGAGGGCAGCAATTATTGAAGATGTCCTTCAAGTCTATAAAAGATCTCCAGAGAGAGCTATTATCTGCTGTGAAACCA
AGAAGAATGTAACTGAAATCGCCATAAATCCACATATAAAATAGAATGCTCAGTGTTACATGGAGACATTGCACAGTCAC
AAAAAGAAATCATGCTTAAAGGCTTCAGAGAAAGTAGTTTTAAGGTGTTGGTGGCAACCAATATGGCTGCCCATAGTGTA
GACATTCCTGAGGCTGACCTGGTGATTCAAAGTTCTCTTCCAGAGAATACTGACTCCTGTATCCATCACTGTTCTGGATA
CACAGATAGAGTTGGTCAAACAGAAATTAGCATATGTTTTTACTAACCAAGAGAAACAGGTCAAGTAAGATATGTGGAAC
AAAAAGCAGGAATTACTTTTAAACATGTAGGCATTCCTTCTATAATGTATTTAGTTGAATCTAAAAGCACGGATGTCATC
TGGTCTCTGGCTTCTGTTTCTTATGCTGCTGTTGATTTTTTTTCACCAACAGTTCAGAGACTGATTGAACAGAAAGAGGC
AGTGGCTGCACTGGCTGCAGCATTAGCTCACATCTCTGATGCATTAAGGTTTGAACCACAATCTTTGATCATCTCTGATA
AGGGGTTTGTGACTAGGACTCTGGAAAGCCCAGAAGAAATATAGGATGTCAGTTGTGCTTGGAAAGAACTTAAAAGAAAG
CTCTATAGTAACACTGTATCACAAATTACTGGAATATGACTTCTAAAAGGAAACATGGGTGTTTGCCCTGATGTTGCCAC
AACTGAATCAGAAAAGTTACAG

Alignment

ORF - retro_pcap_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.11 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVLVLAPTRELASQVSRDFSDITKKLAVACF-YGGTPYGGQFERMRNGIDILVGTPGRIKDHLQSGKLDL
          ..LVL.P.REL......DF...T.KL..ACF.YG...Y..Q.....N..D.L.GTP....D..QSG..DL
Retrocopy KLLVLTPPRELTNHIDKDFKEVTRKLSMACF>YGRSSYESQTNHI*NDVDVLLGTPVVSNDCAQSGQWDL

Parental  SKLKHVVLDEVDQMLDMGFADQVEEILSVA-YKKDSEDNPQTLLFSATCPHWVFNVAKK-YMKTT-YEQV
          SKL.HV.L.EVDQM.D..FA.QVE.I.....Y.....DNPQTLL.SATCPH.........YMK...Y.QV
Retrocopy SKLCHVML-EVDQMVDLRFAEQVEDIIPQT>YRTNPKDNPQTLLLSATCPHGYTKLXXXXYMKSD<YKQV

Parental  DLIGKKTQKTAVTVEHLAIKCRWTHRAAVIGDVIRVYSGYHGRTIVFCETKREAQELSQNASIKQDAQS-
          DL.GK.T.K.A..VEHLAI.C.W..RAA.I.DV..VY.....R.I..CETK....E...N..IK..AQ..
Retrocopy DLVGKITHKDATPVEHLAIQCHWSQRAAIIEDVLQVYKRSPERAIICCETKKNVTEIAINPHIK*NAQC<

Parental  LHGDIPQKQREITLKGFRNGDFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESYIHR-SGRTGRAGRTG
          LHGDI.Q.Q.EI.LKGFR...F.VLVATN.AA...DIPE.DLVIQSS.P....S.IH..SG.T.R.G.T.
Retrocopy LHGDIAQSQKEIMLKGFRESSFKVLVATNMAAHSVDIPEADLVIQSSLPENTDSCIHHCSGYTDRVGQTE

Parental  VCICFYQYKEEYQLTQVEQKAGIKFKRIGVPSATEIIKASSKDAIRYLDSVPPTAVSHFKQSAEKLIEEK
          ..ICFY...E..Q...VEQKAGI.FK..G.PS........S.D.I..L.SV...AV.........LIE.K
Retrocopy ISICFY*PRETGQVRYVEQKAGITFKHVGIPSIMYLVESKSTDVIWSLASVSYAAVXXXXPTVQRLIEQK

Parental  AAVEALAAAL-HIS-ATAVDQRSLISLETGFVTMILKCSVEMSNISYAWKELKEQLGEEIDSKVKGIVFL
          .AV.ALAAAL.HIS.A......SLI....GFVT..L....E....S.AWKELK..L.....S...GI..L
Retrocopy EAVAALAAALAHISDALRFEPQSLIISDKGFVTRTLESPEEI*DVSCAWKELKRKLYSNTVSQITGI*LL

Parental  KGKLGVCFDVPTAAVTEIQ
          KG..GVC.DV.T......Q
Retrocopy KGNMGVCPDVATTESEKLQ

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_346 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.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346 ,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,