RetrogeneDB ID: retro_falb_17

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603175.1:1207165..1208287(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014667
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000013753
• Aliases: None
• Description: None

Sequence

>retro_falb_17
ATGGCAAGCCCAGCCACACCCCCATCCCCTTTAACTGGCCAGCCTCAAACAAGTAACTCGCTAGAGCTGCCCTGTCCTCC
TCGAAGGCCCTTTTCCTTGGCAGTGTTGCAAACCATCCATGCCCACGGCAGAGTGGTGCAGCACAAGCTCACTCAGAGCT
GTGTTTCACTCAGCACACACATTTCTCCCTGGCTGTGCTCTCAGTGCTGGGATCAGTCGGCTCCGTGTGTGTCTGTGTGT
CTGTGTGTTTGTGTGTTTGTGTGTCTGTGTGTTTGCGTGTATGTCTGTGCGGCTCCGTGTGTGTCTGTGTGTCTGTGTGT
TTGTGTGTCTGTGTGTCTGTGTGCATCTGTGTGTGTGTTTGTGTGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTCTG
TGTGTTTGTGTGTATGTCTGTGTGTGTGTTTGTGTGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTCTGTGTGTTTGT
GTGTATGTCTGTGTGTGTGTTTGTGTGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTCTGTGTGTTTGTGTGTATGTC
TGTGTGTGTGTTTGTGTGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTTTCTGTGTGTTTGCGTGTGTGTCTATGTGT
GTGTTTGTGTGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTCTGTGTGTTTGTGTGTATGTCTGTGTGTGTGTTTGTG
TGTGTTTGTGCATTTATTTTGTGTGTTTGTGTGTTTCTGTGTGTTTGTGTGCATTTGCATGTGTGTTTGTGTGTGTGTTT
ATGTGTGTGTTTGCGTATGTTTGTGTCCTTGTATGTGTGTGTTTGTGTGTTTTTGTGTGTCTGTGTTTGTCAGTGTGTTT
GTGTTTTTGCGTGTGTGTTTTTGTGTGTGTCTGTGTGTGATTGTGTGTGTGTGTGTTTGTGTGTTTGCGTGTTTGTGTTT
GTTTTTGTGTGTTTGTGTGTGTTTGTATGTGTGTTTCTGTGTCTGTGTGTTTGTGTGTGTGTCTGTGCATTTATTTTGTG
TGTTTGTGTGTTTGAGTGTTTGTGCATGTGTTTTGTGTGTTTGTGTGTATTTGTGTGTGTTTTCAAGTGTTTTCATGTGT
TT

Alignment

ORF - retro_falb_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 81.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VCVCVCLCVCVCVCVCVCVCLCLCVCLCVCLCVSVCVCVCVCDCVFLCLCVSVCVCVCVCVCVSVCVSVG
          VCV.VCLCVCV.VC...CV..CLCVC..VCLC.SVCV.VCVC....LC.CVSVC.CVC.CVC..V.V...
Retrocopy VCVFVCLCVCVYVCAAPCVSVCLCVCVSVCLCASVCVFVCVCAFI-LCVCVSVCLCVCLCVCLCVFVHLF

Parental  -VSVCVCVSVSVSVCLSVYLCLYLCVCLCVTLCVSVCVSVCVCVSVCVSV-CVCLSFCVCVCVCLSVSLC
          .V.VC.CV.V.V.VC..V.LC.Y..VCLCV..CV.VC.SVCV.V.VC....CVC...CVCVCV...V..C
Retrocopy CVFVCLCVCVYVCVCVCVCLCIYF-VCLCV--CVFVCMSVCVFVCVCAFILCVCVFLCVCVCVYVCVCVC

Parental  VSVCDTVCVCVCVCVSVCVSVGVSVCVCVSVSVSVCLSVYLCLYL---VCVCVSVSVSVCLLVYVCVCLS
          ........VC.CVCV.VC.SV.V.VCVC......VC.....C..L....CVC..V........YVCVC..
Retrocopy LCI---YFVCLCVCVFVCMSVCVFVCVCAFI-LCVCVFLCVCVHLHVCLCVCLCVCLRMFVSLYVCVCVF

Parental  VSVCDTVCVCVCVCV----SVCVCVSVSVSVCLLVYLSVCVCVSVSVSVCLSVYLCVC-LCVCLCVSVCL
          ..VC...CVCV..CV....SVC.CV.V...VC..V...VC.CV.V.V..CL.V..CVC....C.CV..CL
Retrocopy LCVCVCQCVCVFACVFLCVSVCDCVCVCLCVCVFVFVFVCLCVFVCVFLCLCVCVCVCAFILCVCVFECL

Parental  YLCLSVCRCICVCVCVC
          ..C..VC.C..VCV..C
Retrocopy CMCF-VCLCVFVCVFKC

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_17 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000086035	3 retrocopies	retro_drer_25, retro_drer_34, retro_drer_37,
Ficedula albicollis	ENSFALG00000013753	1 retrocopy	retro_falb_17 ,