RetrogeneDB ID: retro_ptro_2735

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:30092826..30093165(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUD31
• Ensembl ID: ENSPTRG00000019451
• Aliases: None
• Description: BUD31 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29629]

Sequence

>retro_ptro_2735
CAGAAAATGCCCTGTGATAATTGGTAGCCAATTGAGGCAACATTGGATGAGTTGGATCAGAAGATGAAGGAAGCTGAGAG
AGAACTTCAGGAAGAAAAGAGGCCAGGGGAGTGTCTCTGGCCCACCTTCAGGATTCCTCATTGGAAATCCTGCTACATCT
TAGAGATGTTTCATTAGCAGAAAGCCATCAGCAGAGAACTGTGTGCGTATTATCTGAAAGAAGATTATGCAGATCCAAAC
CTGACTGCCAAGTGGAAAAGAGACAGTTACAAGGCTTTGTGCTGCCTGTGGTGTGTTCAGACTCAGGATACCAACTTTGG
AACCAACTGCATCTGCCAG

Alignment

ORF - retro_ptro_2735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.83 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKAPPDGWELIEPTLDELDQKMREAETEPHEGKRKVESLWPIFRIHHQKTRYIFDLFYKRKAISRELYEY
          .K.P.D.W..IE.TLDELDQKM.EAE.E..E.KR..E.LWP.FRI.H.K..YI...F...KAISREL..Y
Retrocopy QKMPCDNW*PIEATLDELDQKMKEAERELQEEKRPGECLWPTFRIPHWKSCYILEMFH*QKAISRELCAY

Parental  CIKEGYADKNLIAKWKKQGYENLCCLRCIQTRDTNFGTNCICR
          ..KE.YAD.NL.AKWK...Y..LCCL.C.QT.DTNFGTNCIC.
Retrocopy YLKEDYADPNLTAKWKRDSYKALCCLWCVQTQDTNFGTNCICQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.91 RPM
SRP007412_cerebellum	0.00 RPM	12.83 RPM
SRP007412_heart	0.00 RPM	8.19 RPM
SRP007412_kidney	0.00 RPM	19.93 RPM
SRP007412_liver	0.00 RPM	13.94 RPM
SRP007412_testis	0.00 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2735 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2735 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_672

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006269	2 retrocopies	retro_amel_1325, retro_amel_997,
Bos taurus	ENSBTAG00000020439	1 retrocopy	retro_btau_1066,
Choloepus hoffmanni	ENSCHOG00000004055	1 retrocopy	retro_chof_1013,
Dipodomys ordii	ENSDORG00000000739	1 retrocopy	retro_dord_58,
Equus caballus	ENSECAG00000024151	2 retrocopies	retro_ecab_254, retro_ecab_672,
Ficedula albicollis	ENSFALG00000013804	1 retrocopy	retro_falb_27,
Homo sapiens	ENSG00000106245	1 retrocopy	retro_hsap_4712,
Gorilla gorilla	ENSGGOG00000015119	1 retrocopy	retro_ggor_2928,
Loxodonta africana	ENSLAFG00000012201	1 retrocopy	retro_lafr_24,
Macropus eugenii	ENSMEUG00000006920	1 retrocopy	retro_meug_446,
Microcebus murinus	ENSMICG00000017426	2 retrocopies	retro_mmur_470, retro_mmur_622,
Nomascus leucogenys	ENSNLEG00000011020	1 retrocopy	retro_nleu_2053,
Pongo abelii	ENSPPYG00000017376	2 retrocopies	retro_pabe_3313, retro_pabe_3660,
Pan troglodytes	ENSPTRG00000019451	1 retrocopy	retro_ptro_2735 ,
Pteropus vampyrus	ENSPVAG00000007527	1 retrocopy	retro_pvam_474,
Rattus norvegicus	ENSRNOG00000000989	1 retrocopy	retro_rnor_1852,
Tupaia belangeri	ENSTBEG00000010640	2 retrocopies	retro_tbel_2683, retro_tbel_4119,
Tursiops truncatus	ENSTTRG00000003005	1 retrocopy	retro_ttru_815,