RetrogeneDB ID: retro_falb_29

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603439.1:352987..354571(-)
• Located in intron of: ENSFALG00000005093

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000007384
• Aliases: None
• Description: None

Sequence

>retro_falb_29
GCAGACATTGCCATTGTGGCCCTGTACTTCGTGGTTGTAATGTGCATAGGTTTCTTTGCCATGTGGAAAAACAATCGGAG
CACCGTGAGTGGCTACTTTTTGGCAGGGCGTTCTATGACCTGGGTAGCGATCGGGGCCTCGTTGTTTGTGAGCAATATTG
GAAGTGAACATTTCATTGGGCTCGCAGGATCTGGAGCGGCGAGCGGATTCGCCGTAGGCGCGTGGGAGTTCAACGCCTTA
ATGCTTTTGCAGCTTTTGGGATGGGTCTTCGTGCCAGTCTACATCCGCTCGGGAGTGTACACCATGCCCGAATACTTGTC
CAAGCGGTTCGGAGGGCATAGGATTCAGATCTATTTTGCAGCGTTGTCTCTAATCCTTTATATCTTCACCAAACTCTCGG
TTGACTTGTATTCAGGGGCGCTTTTTATCCAAGAGTCCCTAGGGTGGAACCTGTACCTGTCGGTGATCCTGCTGATCGGC
ATGACGGCGCTGCTGACGGTGACCGGGGGGCTGGTGGCCGTCATCTACACGGACACGCTGCAGGCGCTGCTGATGATCAT
CGGGGCCCTCACGCTCATGTGCATTAGCCTCATAGAGGTCGGCGGGTTCAAGGAAGTGAAAAGGAGGTACATGTTGGCCT
CGCCGAACATCACCTCCATCCTCCTGACCTACAACATCTCCAACACCAACTCGTGCAACGTCGGCCCGAAGCCCGACGCT
CTCAAGATGCTGCGCGAGCCGACGGACGAGGACATTCCCTGGCCCGGGTTTCTGCTGGGACAGACCCCGGCCTCGGTGTG
GTACTGGTGCGCCGACCAAGTCATCGTGCAGAGAGTCCTGGCCGCCAAAAACATCGCTCACGCCAAAGGCTCCACCCTCA
TGGCCGGCTTCCTGAAGCTGCTGCCCATGTTCATCATCGTGGTGCCGGGGATGATCTCCCGCATCCTGTTCGTGGACGAC
ATCGCCTGCATCAACCCCGAGCACTGCTTCCAGGTGTGCGGCAGCCGGGCCGGCTGCTCCAACATCGCCTACCCGCGCCT
GGTGATGAACCTGGTGCCCGTGGGGCTGCGCGGGCTCATGATGGCCGTGATGATCGCCGCCCTCATGAGCGACCTGGACT
CCATCTTCAACAGCGCCAGCACCATCTTCACGCTCGACGTCTACAAGCTGCTGCGCAAGGGCGCGACCTCCCGCGAGCTG
ATGGTGGTGGGCAGGGTCTTCGTGGCCTTCATGGTGGCCATCAGCATCGCCTGGGTGCCCATCATCGTGGAGATGCAGGG
CGGGCAGATGTACCTGTACATCCAGGAGGTGGCCGATTACCTGACGCCGCCGGTGGCCGCCCTGTTCCTCATGGCCATCT
TCTGGAAGCGCTGCAACGAGCAGGGCGCTTTCTACGGCGGCATGGTGGGCTTCGTGCTGGGCGCCACCCGCCTGGTGCTG
GCCTTCTTCTACCGCGCCCCCGAGTGCGACCAGCCCGACACCAGGCCCGGCTTCATCAAGAACATCCACTACATGTACGT
GGCCACGGCGCTGTTCTGGATCACCGGCGCCGTGACGGCGGTGGTGAGCCTGCTGACGCCGCCG

Alignment

ORF - retro_falb_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.27 %
• Parental protein coverage: 80.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADISVIVIYFLLVLAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGIAGTAAAGGI
          ADI.....YF..V...G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.G.AG..AA.G.
Retrocopy ADIAIVALYFVVVMCIGFFAMWKNNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  AIGGFEWNALIFVVILGWIFVPIYVKAGVVTMPEYLKKRFGGKRIQVYLSVLSLILYIFTKISADIFSGA
          A.G..E.NAL.....LGW.FVP.Y...GV.TMPEYL.KRFGG.RIQ.Y...LSLILYIFTK.S.D..SGA
Retrocopy AVGAWEFNALMLLQLLGWVFVPVYIRSGVYTMPEYLSKRFGGHRIQIYFAALSLILYIFTKLSVDLYSGA

Parental  VFIQLAIGLNLYVAIVILLAITALYTITGGLAAVIYTDTLQTFIMVVGSIILTGFAFTEVGGYEAFMQKY
          .FIQ...G.NLY.....L...TAL.T.TGGL.AVIYTDTLQ...M..G...L......EVGG.......Y
Retrocopy LFIQESLGWNLYLSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMCISLIEVGGFKEVKRRY

Parental  MAAVPSNT----TYGGTEVDPKCYTPRSDAFHIFRDATG-DLPWPGLVFGLSIIAMWYWCTDQVIVQRCL
          M.A.P..T....TY...........P..DA....R..T..D.PWPG...G......WYWC.DQVIVQR.L
Retrocopy MLASPNITSILLTYNISNTNSCNVGPKPDALKMLREPTDEDIPWPGFLLGQTPASVWYWCADQVIVQRVL

Parental  SGKNMSHVKAGCVLCGYLKLLPMFIIVMPGMISRILYPDVVACVVPEICQRHCGTAVGCTNIAYPKLVVE
          ..KN..H.K......G.LKLLPMFIIV.PGMISRIL..D..AC..PE.C...CG...GC.NIAYP.LV..
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFVDDIACINPEHCFQVCGSRAGCSNIAYPRLVMN

Parental  LMPNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYTKIRSRPSEKELMLAGRAFMLLLIGISIAWVP
          L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...R......ELM..GR.F......ISIAWVP
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLLRKGATSRELMVVGRVFVAFMVAISIAWVP

Parental  VVQSAQSGQLFDYIQSVTSYLGPPIAAVFLLGVFCKRVNEQGAFWGLIIGLLAGLGRMISEFAYGTGSCV
          .....Q.GQ...YIQ.V..YL.PP.AA.FL...F.KR.NEQGAF.G...G...G..R....F.Y....C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLMAIFWKRCNEQGAFYGGMVGFVLGATRLVLAFFYRAPECD

Parental  APSNCPFIICGIHYLYFAIILFGVTAIVILAVSFMTKP
          .P...P..I..IHY.Y.A..LF..T..V...VS..T.P
Retrocopy QPDTRPGFIKNIHYMYVATALFWITGAVTAVVSLLTPP

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_29 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5,
Choloepus hoffmanni	ENSCHOG00000005940	1 retrocopy	retro_chof_2,
Callithrix jacchus	ENSCJAG00000011369	1 retrocopy	retro_cjac_2033,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29 ,
Homo sapiens	ENSG00000100170	1 retrocopy	retro_hsap_105,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Microcebus murinus	ENSMICG00000008997	1 retrocopy	retro_mmur_1306,
Monodelphis domestica	ENSMODG00000009915	1 retrocopy	retro_mdom_1324,
Mustela putorius furo	ENSMPUG00000012749	1 retrocopy	retro_mputfur_837,
Oryctolagus cuniculus	ENSOCUG00000017569	1 retrocopy	retro_ocun_1633,
Otolemur garnettii	ENSOGAG00000003370	1 retrocopy	retro_ogar_2513,
Ochotona princeps	ENSOPRG00000010458	1 retrocopy	retro_opri_6,
Procavia capensis	ENSPCAG00000015157	1 retrocopy	retro_pcap_3,
Rattus norvegicus	ENSRNOG00000017775	1 retrocopy	retro_rnor_794,
Ictidomys tridecemlineatus	ENSSTOG00000006386	1 retrocopy	retro_itri_13,