RetrogeneDB ID: retro_falb_27

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603308.1:1318559..1318991(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014288
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BUD31
• Ensembl ID: ENSFALG00000013804
• Aliases: None
• Description: BUD31 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29629]

Sequence

>retro_falb_27
ATGGCCAAAGGGAAGAGGAGCAGGACACCTCCCCCTGACGGCTGGGAGCTGATCCACCCCACGCTGGATGAGCTGGATCA
GAAGATGAGAGAAGCAGAGGTGGAGCCACATGAAGGGAAGAGGACAGGGGAGTCCCTCTGGCCCATCTTCAGGATCCACC
ACCAGAAAACACGCTCCATCTTCAAGCTCTTCTACCAGAGGAAAGCAATCAGCAGAGAGCTCTATGAGTACTGCATCAAG
GAGGGCTATGCTGACAGAAACCTGATTGCCCAGTGGAAGAAGCAGGGCTATGAGAACCTCTGCTGCCTGCGCTGCATCCA
GACTCGGGACACCAATTTTGGGACCAGCTGCATCTGCAGGGTGCCCAAAAGCAAGCTGGAAGTGGGCAGAATCATTGAGT
GCACTCACTGTGGGTGCAGAGGCTGCTCTGGG

Alignment

ORF - retro_falb_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKVKRSRKPPPDGWELIEPTLDELDQKMREAETEPHEGKRKVESLWPIFRIHHQKTRYIFDLFYKRKAI
          M.K.KRSR.PPPDGWELI.PTLDELDQKMREAE.EPHEGKR..ESLWPIFRIHHQKTR.IF.LFY.RKAI
Retrocopy MAKGKRSRTPPPDGWELIHPTLDELDQKMREAEVEPHEGKRTGESLWPIFRIHHQKTRSIFKLFYQRKAI

Parental  SRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQTRDTNFGTNCICRVPKSKLEVGRIIECTHCGCR
          SRELYEYCIKEGYAD.NLIA.WKKQGYENLCCLRCIQTRDTNFGT.CICRVPKSKLEVGRIIECTHCGCR
Retrocopy SRELYEYCIKEGYADRNLIAQWKKQGYENLCCLRCIQTRDTNFGTSCICRVPKSKLEVGRIIECTHCGCR

Parental  GCSG
          GCSG
Retrocopy GCSG

Legend:

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

Expression

RNA-Seq

Ficedula albicollis was not studied using RNA-Seq expression data.

ChIP-Seq

Ficedula albicollis was not studied using ChIP-Seq data.

EST

Ficedula albicollis was not studied using EST data.

TSS

Ficedula albicollis was not studied using FANTOM5 data.

Lab

retro_falb_27 was not experimentally validated.

Homology

Retrocopy orthology:

Ficedula albicollis 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 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,