RetrogeneDB ID: retro_falb_10

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: AGTO01003037.1:8934..11415(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000015213
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000008476
• Aliases: None
• Description: None

Sequence

>retro_falb_10
ATGTGCGCGGCGGGGAGGCGCTGGGACCGGAGTCAGCGAGCTCTGCTCTGGGTGATGCTGCTGGCGGCGTGGGAGGCGGC
GTGGGGGCAGCTGCGCTACTCGGTGCCCGAGGAGATGCCCAAGGGCTCGTTCGTGGGCGATGTGGCCAAGGACCTGGGGC
TGCAGCTGCCGGCGCTGATCGAGCGCGGTGTCCGTATAACAGAAAGAGGTAGGACTCAATACTTCTCTCTGCAGGGGAAG
TCGGGCCGTTTAGTGACGGCGGAAAGGATCGACAGAGAGCAGCTGTGCGATCGTGTTCAGCAATGCGTGCTGCGCTGTGA
GCTGATAGTGGAGGGGAAAATGAAGTTTTATGAAATCGAAGTGGAAATCACGGACATTAACGACAACGCGCCCAGCTTCA
AGGAAAGTGAGCTAGAAGAGAGGATTAGCGAGACGACAGCACCAGGTTCGCGGTTTCCCCTGCCAGATGGTTACGACCCG
GATTCTGGACGGCATTCCCTGCAGAGCTACGAGCTGAGCGGTGACGAGCACTTCTCGCTGGCCGTGCAGGCGGGCCCCGG
CGGCGATCAGCGTCCCGAGCTGGTGCTGGCGAAGGCGCTGGACCGGGAGGAGGCGGCGTTTCACGAGCTGGTGCTGAGGG
CGATGGACGGCGGCGATCCGGCACGGACGGGCACGGCTCGGATCCGAGTGACGGTGCTGGACGCGAACGACAACGCGCCC
GTGTTCAGCCAGGCGGAGTACACGGTGCGTGTGCCCGAGGACGTGCCCGTGGGCTCCATCCTCGTCACCCTCACGGCCAC
GGACGCCGATGACGGACTGTACGGGCACGTGGAATACTCGTTAAAAAAACAGTCCGACAGGACATCGAATATCTTCCATC
TGGACTCTGAGACTGGACGTATAACTCTGTTGCAGAGCCTGGACTTCGAGGTAGGTGACTTTTATGAACTGGAGGTGCAG
GCAAGGGACGGCGGCGGCCTTTTCGACACTACCAAAATCACGATCACAGTGACGGACAAAAACGATAACATACCAGTAAT
TTCTGTGCGGTCAGCGCTAAGTGAGATTTCTGAGGACGCCCCATCGGGAACGGTTGTGGCCCTGCTGCACGTACATGATC
GAGACTCGGGAGCTAACGGCGACGTGCGCTGCTCGCTTGACGGTGATGTGCCGTTCAGGCTGCAGAGCTCCCACGGCAGC
TACTACCGCGTGGTGACAGCGAGAGAGCTGGACCGAGAGCAGGTGTCGGAGTACAACGTGACGGTGCGGGCGGCCGACGG
CGGGTCGCCGGCGCTGCAGAGCAGCGCGGTGCTGGCGCTGCGGGTGCTGGACGTGAACGACAACGCGCCGGTGTTCGCGG
AGGAGCGCTACAGCGCGCGGCTGGCGGAGAACAACGCGGCGGGCGCGCTGGTGCTGACGGTGCGCGCGACGGACGCGGAC
TGGGGGCAGAACGCGCGCGTGCGGTACCGGCTGTCGGAGGGGCGGGTGCGGGGCGCGCCGCTGTCGTCGTACGTGTCGGT
GCAGGCGGAGACGGGCGCGCTGTACGCGCTGCGCTCCTTGGACTACGAGCAGGTGCGCGAGCTGCGGCTGTGGGTGCGTG
CGGAGGACGGCGGCGCGCCGGCGCTGAGCAGCAACGTGTCGGTGCTGCTGCTGGTGGTGGACGAGAACGACAACGCGCCG
CAGGTGCTGTACCCGCCGCCGGCCGCGCTGCGGGCGGGCTCGGGCTCGGGCTCGGGCGTTGCGTGGTCGGGCGTGGAGCT
GGCGCCGCGCTGGTCGGAGGCGGGCGCGCTGGTGGCCAAGGTGGTGGCGGTGGACGCGGACGCGGGTCAGAACGCGTGGC
TGTCGTACGAGCTGGCCAAGGCCACGGAGCCGGGGCTGTTCCGCGTGGGGCTGCACAGCGGCGAGGTGCGCACGGCGCGC
TCGCCGCTGGCCCGCGACGCGGCGCGCCACAGCCTGGTGGTGGTGGTGAAGGACCACGGGCGGCCGGCGCTGTCGGCCAC
GGCCACGCTGCAAGTGGTGCTGGCCGAGAGCGTGGCCGAGCTGCTGGCCGAGCTGGGCAGCGCGGCCGACGAGGCGGCGG
CGCCGGGCGAGCCGGCCGTGAGCCTGACGCGCTGGCTCGTGCTGGCCGTGGCCGCCGTGTCGTGCCTCTTCGTCGCCTTC
CTGCTGCTGCTGCTGGCGCTGCGCCTGCGCCGCTGGCGCCGCCAGCAGCTGCTGCCGCCCGACAGCGGCGCCTTGCGCGG
CGTGCCCGTCTCGCACTTCGTGGGCATCGACGGCGTGCGCGCCTTCCTGCAGTCCTACTCGCACGACGTGTCGCTCACGG
CCGACTCGCGCAAGAGCCAGCTGCGCTTCTCGGCCGGCGGCAGCTGCTGCGACACCCTCCCGGCCCGGCCACTGCCCGAC
GAGCCCGCGCCGCTGCTCGGCGACGAGGACCCTGCCGGCGCCCTTGCCGCGGATCCCCCCGCTCTCTCGGTGAGTTTCTG
G

Alignment

ORF - retro_falb_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCAAGRRWGRRQRALLWVMLLAAWEAAWGQLRYSVPEEMPKGSFVGDVAKDLGLQLSALSDRGFRLIERG
          MCAAGRRW.R.QRALLWVMLLAAWEAAWGQLRYSVPEEMPKGSFVGDVAKDLGLQL.AL..RG.R..ERG
Retrocopy MCAAGRRWDRSQRALLWVMLLAAWEAAWGQLRYSVPEEMPKGSFVGDVAKDLGLQLPALIERGVRITERG

Parental  RTQYFALQGKTGHLVTAERIDREELCESVQQCVLRCELIVEGEMKFYEIEVEIMDINDNDPSFQETEKEL
          RTQYF.LQGK.G.LVTAERIDRE.LC..VQQCVLRCELIVEG.MKFYEIEVEI.DINDN.PSF.E.E.E.
Retrocopy RTQYFSLQGKSGRLVTAERIDREQLCDRVQQCVLRCELIVEGKMKFYEIEVEITDINDNAPSFKESELEE

Parental  RVSETTAPGSRFPLREAQDADLGPNSLQSYELSGDEHFSLAVQAGPGGDQRPELVLAKALDREEAAFHEL
          R.SETTAPGSRFPL....D.D.G..SLQSYELSGDEHFSLAVQAGPGGDQRPELVLAKALDREEAAFHEL
Retrocopy RISETTAPGSRFPLPDGYDPDSGRHSLQSYELSGDEHFSLAVQAGPGGDQRPELVLAKALDREEAAFHEL

Parental  VLRAMDGGDPARTGTARIRVTVLDANDNAPVFSQAEYTVRVPEDVPVGSVLVTVSANDADEGQNGQVKYS
          VLRAMDGGDPARTGTARIRVTVLDANDNAPVFSQAEYTVRVPEDVPVGS.LVT..A.DAD.G..G.V.YS
Retrocopy VLRAMDGGDPARTGTARIRVTVLDANDNAPVFSQAEYTVRVPEDVPVGSILVTLTATDADDGLYGHVEYS

Parental  FHKISDRASELFHLDSESGKITVKGGLDFEKVSSHELEVQAQDGGELFDTMKVSILVTDVNDNAPEISIR
          ..K.SDR.S..FHLDSE.G.IT....LDFE.....ELEVQA.DGG.LFDT.K..I.VTD.NDN.P.IS.R
Retrocopy LKKQSDRTSNIFHLDSETGRITLLQSLDFEVGDFYELEVQARDGGGLFDTTKITITVTDKNDNIPVISVR

Parental  SALSEISEDSPSGTVVALLHVQDKDSGPNGEVRCFLDEGVPFRLEKSYKDYYRVVTARELDREQVSEYNV
          SALSEISED.PSGTVVALLHV.D.DSG.NG.VRC.LD..VPFRL..S...YYRVVTARELDREQVSEYNV
Retrocopy SALSEISEDAPSGTVVALLHVHDRDSGANGDVRCSLDGDVPFRLQSSHGSYYRVVTARELDREQVSEYNV

Parental  TVRAADGGSPALQSSAVLALRVLDVNDNAPVFAEERYSARLAENNAAGALVLTVRATDADWGQNARVRYR
          TVRAADGGSPALQSSAVLALRVLDVNDNAPVFAEERYSARLAENNAAGALVLTVRATDADWGQNARVRYR
Retrocopy TVRAADGGSPALQSSAVLALRVLDVNDNAPVFAEERYSARLAENNAAGALVLTVRATDADWGQNARVRYR

Parental  LSEGRVRGAPLSSYVSVQAETGALYALRSLDYEQVRELRLWVRAEDGGAPALSSNVSVLLLVVDENDNAP
          LSEGRVRGAPLSSYVSVQAETGALYALRSLDYEQVRELRLWVRAEDGGAPALSSNVSVLLLVVDENDNAP
Retrocopy LSEGRVRGAPLSSYVSVQAETGALYALRSLDYEQVRELRLWVRAEDGGAPALSSNVSVLLLVVDENDNAP

Parental  QVLYPPPAALRAGSGSGSGVAWSGVELAPRWSEAGALVAKVVAVDADAGQNAWLSYELAKATEPGLFRVG
          QVLYPPPAALRAGSGSGSGVAWSGVELAPRWSEAGALVAKVVAVDADAGQNAWLSYELAKATEPGLFRVG
Retrocopy QVLYPPPAALRAGSGSGSGVAWSGVELAPRWSEAGALVAKVVAVDADAGQNAWLSYELAKATEPGLFRVG

Parental  LHSGEVRTARSPLARDAARHSLVVVVKDHGRPALSATATLQVVLAESVAELLAELGSAADEAAAPGEPAV
          LHSGEVRTARSPLARDAARHSLVVVVKDHGRPALSATATLQVVLAESVAELLAELGSAADEAAAPGEPAV
Retrocopy LHSGEVRTARSPLARDAARHSLVVVVKDHGRPALSATATLQVVLAESVAELLAELGSAADEAAAPGEPAV

Parental  SLTRWLVLAVAAVSCLFVAFLLLLLALRLRRWRRQQLLPPDSGALRGVPVSHFVGIDGVRAFLQSYSHDV
          SLTRWLVLAVAAVSCLFVAFLLLLLALRLRRWRRQQLLPPDSGALRGVPVSHFVGIDGVRAFLQSYSHDV
Retrocopy SLTRWLVLAVAAVSCLFVAFLLLLLALRLRRWRRQQLLPPDSGALRGVPVSHFVGIDGVRAFLQSYSHDV

Parental  SLTADSRKSQLRFSAGGSCCDTLPARPLPDEPAPLLGDEDPA
          SLTADSRKSQLRFSAGGSCCDTLPARPLPDEPAPLLGDEDPA
Retrocopy SLTADSRKSQLRFSAGGSCCDTLPARPLPDEPAPLLGDEDPA

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_10 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002556	6 retrocopies	retro_eeur_140, retro_eeur_291, retro_eeur_527, retro_eeur_630, retro_eeur_631, retro_eeur_637,
Ficedula albicollis	ENSFALG00000008476	1 retrocopy	retro_falb_10 ,
Pelodiscus sinensis	ENSPSIG00000004827	2 retrocopies	retro_psin_14, retro_psin_43,