RetrogeneDB ID: retro_pcap_399

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_67796:1410..2191(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSPCAG00000014356
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 [Source:HGNC Symbol;Acc:9565]

Sequence

>retro_pcap_399
AGAATAGGCCAGGCTGGAAAGAAGAAACCTGTTGCTGGTGTGCTTTTGGGGTCAATACAAAAGAAAGTACTGGATGTATC
CAACAGTTTTGCGGTCCCTTTTGATGAAGATGATCAAGATGACTCTGGTTTTTAGACCATGATTATTTAGAAAACATGTA
TGGAATGTTTAAGAAGGTCAATGCTAGGGATAGAATACTTGGGTGGTACCAGACAGGCCCTAAATTACACAAGAATGGCA
TCGCCATCAATGAACCCATGAAAAGATACTGACCTACCTCAGTATTAGTGATTATTGATGTGAAGCCAAAGACCTGGGGC
TCCCCACAGAAGCTTATATTTCAGTGGAAGAAGTTCGTGATGATAGAACTCCAGCCTCAAAAACGTTTAAGCGTGTAACT
AGTGAAACTGGGGTGGAGGAAGCTGAAGAAGCTGTAGTCGAACACTTGTTATGAGACATCAAAGACACTTCAGTGGATAC
TCTTTCCCAGTGTATCACAAACTAGGTCCGTGGTTTGAAGAGTCTGAACTCCAAGCTTCTGGATATCAAGAGCTACCTGG
AGAAAGAGGTCACTGGCAAGCTACGCATCAACAACCAGATCATCAACCAGTTGCAAGACGTCTTCAACCTGCTGCCAGAA
GTCAGCCTGCAGGAGTTTGTTAAAGCCTTTTACCTGAAGACCAGCGACCACATGGTGGTAGTATACCTGACTCCCCTGAT
TCCTTCTGTCATAGCCCTGCACAACCTCATCAACAGCAAGATTGCCTACTGGGATGCAGAG

Alignment

ORF - retro_pcap_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 80.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDS-VWFLDHDYLENMYGMFKKVNARERIVG
          RIG..G..K.V.GVLLGS.QKKVLDVSNSFAVPFDE.D..D...WFLDHDYLENMYGMFKKVNAR.RI.G
Retrocopy RIGQAGKKKPVAGVLLGSIQKKVLDVSNSFAVPFDE-DDQDD<LWFLDHDYLENMYGMFKKVNARDRILG

Parental  WYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKP-KDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEI
          WY.TGPKLHKN.IAINE.MKRY.P.SVLVIIDVKP.KDLGLPTEAYISVEEV.DD.TP.SKTF..VTSE.
Retrocopy WYQTGPKLHKNGIAINEPMKRY*PTSVLVIIDVKP<KDLGLPTEAYISVEEVRDDRTPASKTFKRVTSET

Parental  GAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGQLPINHQIIYQLQD
          G.EEAEE..VEHLL.DIKDT.V.TLSQ.ITN.V.GLK.LNSKLLDI.SYLEK..TG.L.IN.QII.QLQD
Retrocopy GVEEAEEAVVEHLL*DIKDTSVDTLSQCITN*VRGLKSLNSKLLDIKSYLEKEVTGKLRINNQIINQLQD

Parental  VFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRDAE
          VFNLLP.VSLQEFVKAFYLKT.D.MVVVYL..LI.SV.ALHNLIN.KIA..DAE
Retrocopy VFNLLPEVSLQEFVKAFYLKTSDHMVVVYLTPLIPSVIALHNLINSKIAYWDAE

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_399 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399 ,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Ictidomys tridecemlineatus	ENSSTOG00000013123	1 retrocopy	retro_itri_1665,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,