RetrogeneDB ID: retro_falb_6

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603236.1:2076417..2077815(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014194
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000011278
• Aliases: None
• Description: None

Sequence

>retro_falb_6
ATGTGCCGAGAGTCCCACTGGAAATGCCTCCTCCTCTCCATCCTCATGTATGGCTGCCTGGGTGCAGTGGCCTGGTGTCA
GCTGGCCAGAGTCACCAAGCTCAGCTTCGATAGCTCCTTCAAGGGCAAGTCTATGATCTACCACGACAGCCCGTGTTCGG
ACGGCTACGTTTACATCCCACTGGCCTTCCTCTCCATGCTCTATGTGGTGTACCTGGTGGAGTGCTGGCACTGCCACGTC
AAGAGGGAGCTGCAGTACAAGGCAGACGTGGACAGCGTGTACGAGTGCATCAGCCGCATGCAGCAGGCCACTCCGTGCAT
CTGGTGGAAGGCCATCAGCTACCACTTCGTGCGCAGGACCCGGCAGGTGACGCGCTACCGCAACGGCGACGCCTACACCA
CCACGCAGGTCTACCACGAGCGGGTCAACACCCACGTGGCTGAAGCCGAGTTTGACTACTCCCACTGCGGGTACAAGGAC
ATCTCCAAGGAGCTCCTGGGCTTGGAGAGCTATACAGCCACCAAGCTGAGGTTCACCAAGTGCTTCAGCTTTGCCAACAT
TGAGTCTGAGAACTCTTACCTGACTCAGAGAGCTCATTTCTTCACGGAGATCGAGGGGCTAGATGACTACATGGAGGTGA
GGGAAGGCATGCAGCTCAAAAACGTGGATTTTAAAGAGCTCATGATGGCCTACGGAGACCCGGACCACCTGCCGTGGTAC
GTGTCCCATTATGCCTTCTGGGTGGCAGCCGTCCTGATGGTCTCGTGGCCGCTCAGGGTGCTCATAGAGTACCGGACTGC
TTACGTGCACTACCACGTGGAGAAGCTGCTGGGGCTGGAGTACACGGCGCCCGCCGCGGCCGAGGAGCCCCTGTACCGGT
ACCGCATGCCCCGGGACGCCACGCAGGACAGCACCGAGCTGGAGTGGCACATCTGCACCAACCGGCAGCTGATCCCCAGC
TACTCGGAGGCCGTGCTCATGGACCTGGCCGGCTCCCCGGCCTACAGCAGCTACGCCGCGTGTCGCTACGGCGACGCGGC
CCACGGCTGCGAGCGCTGCCACCGGGCCTCCAGCACCTCCTCCATCTTCTCGCGCCACGCTTTCCACAGCTGCAGCGGCA
ACTCGCGCCTCTCCCTCAACACCAGCCGCTTCTCGCTCTGCCGCGTCCACGGCTCGCACAGGACAGGCCTCTGGCGGAGC
CGCAGCAGCAGCATCGCCGAGCGGGGCTGCCAGGATGAGCGGTGCTGCTCCTACTCCAGCCAGCTGGCTGTCAACGAGAG
CCCCCCGACCTACCACGACGCGCGCTTCTTCCCCGTCCTCATCGTGCACAGGCCGGAGGGGCAGGACAGGCGGCATTTCT
ACGTCAGGCGCTCCTCCTGCCTGGAAACCTCCCTGTGA

Alignment

ORF - retro_falb_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYGCMGAMTWCHVTKVTRLTFDSAYKGKSMMYHDSPCSNGYVYIPLAFLVMLYVVYLVECWHCYTRNELQ
          MYGC.GA..WC....VT.L.FDS..KGKSM.YHDSPCS.GYVYIPLAFL.MLYVVYLVECWHC....ELQ
Retrocopy MYGCLGAVAWCQLARVTKLSFDSSFKGKSMIYHDSPCSDGYVYIPLAFLSMLYVVYLVECWHCHVKRELQ

Parental  YKVDVESVHERVQRMQQATPCIWWKAISYHYVRRTRQVTRYRNGDAYTTTQVYHERVNTHVAEAEFDYSN
          YK.DV.SV.E...RMQQATPCIWWKAISYH.VRRTRQVTRYRNGDAYTTTQVYHERVNTHVAEAEFDYS.
Retrocopy YKADVDSVYECISRMQQATPCIWWKAISYHFVRRTRQVTRYRNGDAYTTTQVYHERVNTHVAEAEFDYSH

Parental  CGVKDISKDLIDLESYPATRLRFTKCFSFANVESENSYLTQRARFFTENEGLDDYMEAREGMHLKNVDFK
          CG.KDISK.L..LESY.AT.LRFTKCFSFAN.ESENSYLTQRA.FFTE.EGLDDYME.REGM.LKNVDFK
Retrocopy CGYKDISKELLGLESYTATKLRFTKCFSFANIESENSYLTQRAHFFTEIEGLDDYMEVREGMQLKNVDFK

Parental  EYMVAFSDPDNLPWYVSHYVFWVAALLTLSWPLRVLNEYRTSYVHYHVEKLFGFDYVAVTPAEERSFCRR
          E.M.A..DPD.LPWYVSHY.FWVAA.L..SWPLRVL.EYRT.YVHYHVEKL.G..Y.A...AEE.....R
Retrocopy ELMMAYGDPDHLPWYVSHYAFWVAAVLMVSWPLRVLIEYRTAYVHYHVEKLLGLEYTAPAAAEEPLYRYR

Parental  MPRVNTVDSTELEWHIRSNQQLVPSYSEAVLMDLVGLSGCTSYSACRYGGYRQNCERCHRTISSSSIFSR
          MPR..T.DSTELEWHI..N.QL.PSYSEAVLMDL.G.....SY.ACRYG.....CERCHR..S.SSIFSR
Retrocopy MPRDATQDSTELEWHICTNRQLIPSYSEAVLMDLAGSPAYSSYAACRYGDAAHGCERCHRASSTSSIFSR

Parental  SALSICNGSPRIPFSSSRFSLGRLYGSRRSCLWRSRSGSLNEQSCPTEQTRLSSQVTVEEEDPPPYQDAL
          .A...C.G..R.....SRFSL.R..GS.R..LWRSRS.S..E..C..E.....S......E.PP.Y.DA.
Retrocopy HAFHSCSGNSRLSLNTSRFSLCRVHGSHRTGLWRSRSSSIAERGCQDERCCSYSSQLAVNESPPTYHDAR

Parental  YFPVLIVHRNEGCLNHDHRHLH-RNGSCVETSL
          .FPVLIVHR.EG....D.RH...R..SC.ETSL
Retrocopy FFPVLIVHRPEG---QDRRHFYVRRSSCLETSL

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_6 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000011278	1 retrocopy	retro_falb_6 ,