RetrogeneDB ID: retro_falb_20

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603174.1:3334067..3334434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSFALG00000000924
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_falb_20
CACAGAAAACATCCCAGAGGACATGGCAATAATGCTGGTGGTATGCAACATCACAGGATGAACTTCAACAAGCATCACTC
TGGTTACTTCAGAAAAGTAGGCATGATACACTGTCACTCGAAAAGAAACCAAAAAATTCTGTGCTACTGTCAATTTGGAA
ACTGGGGAGACTTTGAAGCTAATAGAAAAGGTTCAATTACATGAAAAATGAGGCCAGACTGGCCACAGTCACTGATATTA
TGCACTCAGGCTAAGTGCTAGGCAAAGGGAAGCTGCCCAAGCAACTCCCCACTTGTGAAAGCAAAGTTCTTCAGTAGAAG
CGTAGAGGGGAAAAATCGAAGAAGTTGGTGGTGCTTGTGTGTTCGTG

Alignment

ORF - retro_falb_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.42 %
• Parental protein coverage: 97.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HRKHPGGRGN-AGGLHHHRINFDKYHPGYFGKVGMRHYHLKRNQKFC-PTVNLDKLWTLVSEQTRLNYAK
          HRKHP.G.GN.AGG..HHR.NF.K.H.GYF.KVGM.H.H.KRNQK.........KL..L.S...R.NY.K
Retrocopy HRKHPRGHGNNAGGMQHHRMNFNKHHSGYFRKVGMIHCHSKRNQKIL<VLLSIWKLGRL*S**KRFNYMK

Parental  NEAGLAPVIDVVRSGYYKVLGKGKLPKQ-PVIVKAKFFSRRAE-EKIKEVGGACVLV
          NEA.LA.V.D...SG...VLGKGKLPKQ....VKAKFFSR..E..KI.EVGGACV.V
Retrocopy NEARLATVTDIMHSG*--VLGKGKLPKQ>SPLVKAKFFSRSVE>GKIEEVGGACVFV

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_20 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 19 parental genes, and 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20 ,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162, retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268,
Mustela putorius furo	ENSMPUG00000012532	3 retrocopies	retro_mputfur_118, retro_mputfur_1362, retro_mputfur_464,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Nomascus leucogenys	ENSNLEG00000017535	1 retrocopy	retro_nleu_102,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677, retro_sscr_769, retro_sscr_809,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,