RetrogeneDB ID: retro_pcap_366

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_50964:1393..2039(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSPCAG00000011543
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_pcap_366
AAAATGTTTATTGGAGGCTTGAGCTGGGATACAAGCAAGAAAGATTTCACTGAACATTTGTCTCGATTTGGAGACAATGT
AGACTGCACAATTAAAACACATCCAGTCACTGGATGCTCAAGTGGATTTGGATTTGTGCTTTCCAAAGATGCTGCTAGTG
TTGATAAGGTTTTGGAACTGGAAGAACACAAGCTGGACGGCAAACTGATAGACCCTAAAACGGCCAAAGCTTTAAAAGGG
AAGGAGTCCCCCAAAAGGTTTTTGTGCATGGATTGAGCCCAGATACTTCTGAAGAACAAATTAAAGAATATTCTGGTGCT
TTTGGAGAGAATGAAAACACTGAACTTCCCATGGATACAAAGAGAAACGAAAGAAGAGGATTTTGTTTTAACGCATATAC
AGATGAAGAGCCAGTAAACAAATTGCTAGAAAGCAGGTATCATCAGATAGATTCTGGAAAGCGTGAAATCAAAATTCTAC
AACCTGAAGAGGTATACAGGTGCAACAGCAACAACAAAAAGGAGGAAGAGTTGCCATAGCTGGTGGATGAGATGGTACTA
GGGGTGGTGGATGAGGTCAGGGCCAAAACTGGAACCCCAAATTTAATAACTATTATGATCAAGGATATGGAAATTACAAT
AGTGCC

Alignment

ORF - retro_pcap_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 51.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLI
          KMFIGGLSWDTSKKD.TE.LSRFG..VDCTIKT.PVTG.S.GFGFVL.KDAASVDKVLEL.EHKLDGKLI
Retrocopy KMFIGGLSWDTSKKDFTEHLSRFGDNVDCTIKTHPVTGCSSGFGFVLSKDAASVDKVLELEEHKLDGKLI

Parental  DPKRAKALKGKEPPK-KVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPV
          DPK.AKALKGKE.PK.KVFV.GLSPDTSEEQIKEY.GAFGE.EN.ELPMDTK.NERRGFCF..YTDEEPV
Retrocopy DPKTAKALKGKESPK<KVFVHGLSPDTSEEQIKEYSGAFGENENTELPMDTKRNERRGFCFNAYTDEEPV

Parental  KKLLESRYHQIGSGKCEIKVAQPKEVYR-QQQQQQKGGRGATAGGRGGTRGRGRGQGQNWNQGFNNYYDQ
          .KLLESRYHQI.SGK.EIK..QP.EVYR..QQQQQKGGR.A.AGG..GTRG.G.GQGQNWN..FNNYYDQ
Retrocopy NKLLESRYHQIDSGKREIKILQPEEVYR<VQQQQQKGGRVAIAGG*DGTRGGG*GQGQNWNPKFNNYYDQ

Parental  GYGNYNSA
          GYGNYNSA
Retrocopy GYGNYNSA

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_366 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 15 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366 ,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,