RetrogeneDB ID: retro_pcap_22

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_33078:9627..11658(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000001411
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KIF2A
• Ensembl ID: ENSPCAG00000005089
• Aliases: None
• Description: kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]

Sequence

>retro_pcap_22
ATGGCCAGCCAGTTCTGCCTCCCCCTTGCCCCGTGTCTCTCGCCCCTGGAACCCTCGAAATCACATTTCGGAGATGTCCA
AGTGGGCATCTGTGTGATGATAAAGCGCAGCGACGGGCGGATCCACCTCGCTGTGGTCACGGAGATCAACAGAGAAAATG
CTTGGGTCACGGTAGAGTGGGTCGAGAAAGAAGTCAAAAAAGGCAAGAAGATTGATCTAGAGACCATACTCCTGCTGAAT
CCAGCGCTAGTGTCGGCTAAACACCCCATGCTGCCTAAGCCGTTGCTCACTTCGTCTCTAGCCTCCCCTTCAGCCACTGG
AGACCAGCGTCTGGCCACACAATGGATGGTGAAGATCCCCCAGAAAAATGAAACACCCTCAGGGGATGGCCTGGTGGTGG
AGATACCCAGCAGCCCTTGCTTGATGAAGCAGAAAAAGTCAACTTGTGTCCGAGAAATTGAGAAACTGCAGAGGCAGAGA
GAGGAACGCAGGCGGCAGCAGCTGGAGATCCGAGCCCAGCGCGCTCAAGACATCAACTCAGGAAACCCCAACTCAGAGAT
CATGCGCATGATCGCCGAGTGCCGCCGCCACCTGGACAGCAGCAAGCTGTCCGGCCGGGAGCCCCCGGAAGACCACCGCA
TCTGCGTCTGCGTGAGGAAACGGCCTCTCAACCAGCGAGAAACCGTCTTGAAGGACCTGGATATCATAACCATCCCTTCC
AACAACGTAGTCATGGTCCACGAGTCCAAGCAAAAGGTGGACCTCACGCGCTACCTGGAGAACCAGACCTTCTGCTTTGA
CCACGCCTTTGATGACACTGCTTCCAACGAGTTAGTGTACCAGTTTACCGCTCAGCCGCTGGTGGAGTCGATCTTCCGCA
GGGGCATGGCCACCTGCTTTGCCTATGGGCAGACAGGCAGTGGGAAAACACACACCATGGGTGGAGCCTTTTCAGGAGAG
GAGCAAGACTGCTCTAAAGGCATCTTTGCCTTGGTAGCGCAGGATGTCTTCCTCTTGCTCAAAAATCCCTCCTACGAGAA
GCTCGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGAGGCAAGGTGTATGACTTACTGAACTGGAAGAAGAAGC
TGCAAGTCCTTGAAGATGGCAATCAGCAAATGCAGGTAGTAGGGCTGAGGGAACAGGAGGTGTGTTGTGTAGAGGACGTT
CTAAGCCTCGTGGAGCTAGGGAACAGCTACCGGACTTCTGGACAGACATCTGTCAACGCCCACTCTTCCAGGAGCCACGC
GGTGTTTCAGATCATCTTGAAGTCGCAAGGGGAGGTGCATGGCAAGTTTTCCCTTGTTGATTTAGCTGGGAATGAGAGGG
GAGCAGATACTGCCAAGGCCAACCGGAAGAGGCAGCTGGAGGGGGCGGAGATAAACAAGAGTCTTCTGGCTCTTAAGGAA
TGCATCCGGGCTTTGGGTCAGAATAAACCTCATACTCCATTCAGAGCCAGCAAACTCACGCAGGTGCTCCGGGACTCTTT
CATAGGCCCAAACTCCTCCACCTGCATGATTGCAACTATCTCACCAGGGATGGCCTCTTGCGAAAACACTCTCAACACTT
TAAGGTATGCCAACAGAGTAAAACAAATAACTCTCTATGTCAGACCCCACCACCGTAGCCTCTGTCCAGTTGGACGTGAG
TCACCAAACTTGTCGGAAAAGCACGTGAGTAATTCAGAAATGTCCCTTCAGAGCGATGAATTTATTAAAATACCATGTAT
ACCACATGGTATACAGAGCGAGGAGAAGACTGAAGGAGAAATTGAAAAATTTGCCACTCCGTCAGTGGAGAACGTTATGT
CGTCTTGGAAGGAAGCCCATCAGTGGCCCACGAACATACAAGAGACAGTGAATGGGGTAAACTATGATGTCGATTTTTGC
ATTTCCCAGTTATTGGCCATTTTGGATCAGAAAATTGGTGTTCTGACTGAGGTTCAAGAGAAACTGCGATTATTACAGGC
TGACTTCAGAAAGAAGAGCAAGGTAGAGTGA

Alignment

ORF - retro_pcap_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.68 %
• Parental protein coverage: 55.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRKSNC-QEVEKLQEKXXXXXXXXXXXXXXXXXDVDATNPNYEIMCMIRDFRGSMDYRPLTTADPIDEHR
          ..KS.C..E.EKLQ...................D....NPN.EIM.MI...R...D...L....P...HR
Retrocopy QKKSTCVREIEKLQRQREERRRQQLEIRAQRAQDINSGNPNSEIMRMIAECRRHLDSSKLSGREPPEDHR

Parental  ICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
          ICVCVRKRPLN..ET..KDLD.ITIPS..VVMVHE.KQKVDLTRYLENQTF.FD.AFDD.A.NE.VY.FT
Retrocopy ICVCVRKRPLNQRETVLKDLDIITIPSNNVVMVHESKQKVDLTRYLENQTFCFDHAFDDTASNELVYQFT

Parental  ARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
          A.PLVE.IF.RGMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGI.AL.A.DVFL.LK.P.Y.KL.L.VY
Retrocopy AQPLVESIFRRGMATCFAYGQTGSGKTHTMGGAFSGEEQDCSKGIFALVAQDVFLLLKNPSYEKLDLKVY

Parental  ATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVRCVEDVLKLIDIGNSCRTSGQTSANAHSS
          .TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGL.E.EV.CVEDVL.L...GNS.RTSGQTS.NAHSS
Retrocopy GTFFEIYGGKVYDLLNWKKKLQVLEDGNQQMQVVGLREQEVCCVEDVLSLVELGNSYRTSGQTSVNAHSS

Parental  RSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
          RSHAVFQIIL...G..HGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NKPHTP
Retrocopy RSHAVFQIILKSQGEVHGKFSLVDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQNKPHTP

Parental  FRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKE
          FRASKLTQVLRDSFIG.NS.TCMIATISPGMASCENTLNTLRYANRVK.
Retrocopy FRASKLTQVLRDSFIGPNSSTCMIATISPGMASCENTLNTLRYANRVKQ

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_22 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 24 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000009519	1 retrocopy	retro_apla_3,
Bos taurus	ENSBTAG00000015022	1 retrocopy	retro_btau_180,
Choloepus hoffmanni	ENSCHOG00000007888	1 retrocopy	retro_chof_1348,
Cavia porcellus	ENSCPOG00000009393	1 retrocopy	retro_cpor_72,
Dipodomys ordii	ENSDORG00000006335	1 retrocopy	retro_dord_763,
Equus caballus	ENSECAG00000019810	1 retrocopy	retro_ecab_32,
Homo sapiens	ENSG00000068796	1 retrocopy	retro_hsap_69,
Gorilla gorilla	ENSGGOG00000004774	1 retrocopy	retro_ggor_68,
Macaca mulatta	ENSMMUG00000000399	1 retrocopy	retro_mmul_145,
Monodelphis domestica	ENSMODG00000019605	1 retrocopy	retro_mdom_242,
Mus musculus	ENSMUSG00000021693	1 retrocopy	retro_mmus_68,
Nomascus leucogenys	ENSNLEG00000002865	1 retrocopy	retro_nleu_2329,
Oryctolagus cuniculus	ENSOCUG00000010466	1 retrocopy	retro_ocun_156,
Otolemur garnettii	ENSOGAG00000000527	5 retrocopies	retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps	ENSOPRG00000011768	1 retrocopy	retro_opri_815,
Procavia capensis	ENSPCAG00000005089	1 retrocopy	retro_pcap_22 ,
Rattus norvegicus	ENSRNOG00000014000	2 retrocopies	retro_rnor_1284, retro_rnor_47,
Sorex araneus	ENSSARG00000007768	1 retrocopy	retro_sara_457,
Sarcophilus harrisii	ENSSHAG00000001950	1 retrocopy	retro_shar_30,
Ictidomys tridecemlineatus	ENSSTOG00000012710	1 retrocopy	retro_itri_40,
Tupaia belangeri	ENSTBEG00000009396	1 retrocopy	retro_tbel_761,
Tarsius syrichta	ENSTSYG00000002115	1 retrocopy	retro_tsyr_1791,
Vicugna pacos	ENSVPAG00000008864	1 retrocopy	retro_vpac_572,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,