RetrogeneDB ID: retro_pcap_151

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_11653:5982..7170(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000003555
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSPCAG00000005962
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_pcap_151
AAAGATTGTGAAAAATGTCCTATTCCTAAACCAATCTGTACATCTGAAGATGCTTTTAGATGTTATCTTGAAATTATAGA
CAGCATTAAAAAAACAGGTGTTCTAAAACCACCATTTCAAGAACAGGCATGGCCCATAATTCTCCAAGGAATACATTTTA
TCGGGGTTACCCAAACTGGAAGAGGTGATGCATTGCCCTGCTTAATGCCTGAGTTTATTCATCTCAGTTTTCAACCAACA
CATAGAGACATGTGGGAGAGACCTGGCACGCCAGTGCTTACACCAACCAGAGAATTAGCCATTCAAGTGGAAGGTGTATG
TACTAAGTGTTCATATAAAGACCTTAAAAGTATTTGTGTATATGATGGTAGCAACAGAGAACAAACACATGACATTACCA
AAGCTGCAGATGTCACTACTGAAACTTCTGGCCAACTAAATGATCTGCAAATGAATAAGTTTGTCAGCCTAAGAAGCATC
GCCCATTTGGTGTTAGATAAAATGCTTGACTTGGGGTGTGAACACCAGATAAAGATGATTTTATTAGACATGCACCCAGA
TAGGCAAACCGCTATGACGGGTGCCACATGGCCTGACAGTGCTCGTCAATTAGCACAATCTTATTTGAAAGAACTAATGA
TTGTATATGCAGGTACTCTGGATCCTGCTGCAGTAAATACAGTGACCCAAAATATAATCATTAGCACAGAAGAAAAGAAA
AGATCTCTTGACCAAGAGCTTTTACAAAGCATGTCAACCAAAGTCATTGTGTTTGTCAACAGAAAACTTATTGCTGATGA
TTTGTCAAGTGAGTTAAGTCTCCAGAGTAGTCTTGTGCAGTTGCTGCACAGCAACAGAGAACAGAGTGATCAGAAGCAAG
CACTAGATGATTTTAAAAGTGGTAAAGGGAAGATACTGATTGCTACTGAAACTGCATCCAGAGGCTTGGACGTTCATGAT
GTAATACACGTATATAACCACAATCTTCCACAAAATATCGAAGAACACGTCCACCCAGTAGGGTGCACCAGAAAAGCAAG
GAAGATTGGCACATCAGTTACCCTTATCACTTATGAAGACTGGACAATTGCCAGCGAATTGATTAAAATTCTGAAAAGAG
TGAATCAGTCTGTCCCAGACAAGCTTGCAATAATGGCTGACAGATATGAGGAACACGAGCAACACAAG

Alignment

ORF - retro_pcap_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.96 %
• Parental protein coverage: 62.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDGEKRPIPNPTCKFEDAFQCYPEVMENIKRAGFQKPTPISQAWPIVLQGVDLIGVAQTGTGKTLSYLMP
          KD.EK.PIP.P.C..EDAF.CY.E....IK..G..KP....QAWPI.LQG...IGV.QTG.G..L..LMP
Retrocopy KDCEKCPIPKPICTSEDAFRCYLEIIDSIKKTGVLKPPFQEQAWPIILQGIHFIGVTQTGRGDALPCLMP

Parental  GFIHLDSQPLARDKRLGPGMLVLTPTRELALQVEAECSKYSYKGLKSVCIYGGGDRDGQIQDLTKGVDII
          .FIHL..QP..RD....PG..VLTPTRELA.QVE..C.K.SYK.LKS.C.Y.G..R..Q..D.TK..D..
Retrocopy EFIHLSFQPTHRDMWERPGTPVLTPTRELAIQVEGVCTKCSYKDLKSICVYDGSNRE-QTHDITKAADVT

Parental  IATPGRLNDLQMNNFVNLKSITYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIMTSATWPHAVRRLAE
          ..T.G.LNDLQMN.FV.L.SI..LVL...DKMLD.G.E.QI..ILLD..PDRQT.MT.ATWP...R.LA.
Retrocopy TETSGQLNDLQMNKFVSLRSIAHLVL---DKMLDLGCEHQIKMILLDMHPDRQTAMTGATWPDSARQLAQ

Parental  SYLRDPMIVYVGTLDLVAVSTVKQNVIVTTEEEKRSHIQIFLESMSPKDKVIVFVSRKAVADHLSSDLIL
          SYL...MIVY.GTLD..AV.TV.QN.I..TEE.KRS..Q..L.SMS.K..VIVFV.RK..AD.LSS.L.L
Retrocopy SYLKELMIVYAGTLDPAAVNTVTQNIIISTEEKKRSLDQELLQSMSTK--VIVFVNRKLIADDLSSELSL

Parental  RRISVESLHGNREQSDREKALENFKTGKVRILIATDLASRGLDVNDVTHVYNYDFPRNIEEYVHRVGRTG
          ....V..LH.NREQSD...AL..FK.GK..ILIAT..ASRGLDV.DV.HVYN...P.NIEE.VH.VG.T.
Retrocopy QSSLVQLLHSNREQSDQKQALDDFKSGKGKILIATETASRGLDVHDVIHVYNHNLPQNIEEHVHPVGCTR

Parental  RAGRTGVSITLITRSDWRVATELINILERANQNVPEDLVSMAERYKANKQKK
          .A...G.S.TLIT..DW..A.ELI.IL.R.NQ.VP..L..MA.RY....Q.K
Retrocopy KARKIGTSVTLITYEDWTIASELIKILKRVNQSVPDKLAIMADRYEEHEQHK

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_151 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 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151 ,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,