RetrogeneDB ID: retro_falb_3

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603222.1:715154..716054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014827
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000001547
• Aliases: None
• Description: None

Sequence

>retro_falb_3
CAGCAATCCAATGTCACTTCATACGGGACCATAATTTTGGCCATCATCAGCCTGGAGACATTTGCTGGCGTGTGGATAAA
TGCTTTCATCGTTTGTGTGCTCTGCATTGGCTGGGTCAAAAAGAAAACCGTGAACTCTAATGAGAAGATCTTGCTGCTGC
TGGGATGCTGCAGGTTTTGCTATTTGTGCATTTCATGGGCATATTCATTTCTCTCAAGAATTTATCCAAATTACCTTTAT
GTTCATACCATACTTCAACTAACTGTATTTTTTCAAACATTATTTAATTATTCCAACTTGTGGGTTTCAGCCTGTCTTTG
TGTTTTTTATTGTATAAAAATTGCCAATTTCAGAAACAGCTTCTTCAACTACCTGAAAGTAAAAATTGACAGGATGGTGC
CATGGCTCTTGTTGGGGTCTGGGATTTTAGCCTTGGCTATGGGCATCATTGCCTACGACATCGCTGATAAACCGCACTGC
AGCAACCACAATTCCAGCAGACAAGGAAATTTTGGGAAAGCAAGTATCAGAATGGATAAACATTTTTTCCCTTCTTTTTT
TCTTGCTGGCATTGGATATGCTGCTTCATTCATGGCAGTCATCTTTGCTGCTGTTCTCCTTCTCTTCTCTCTCTGGAAAC
ACAAATGCAAGATGCAGACAAACTCCTTGAAGGACCTCAGCGTGGATGCCCACATTAGAGCCATGAAATCTATTCTCTCC
TTCTTAGTGATGTACAGCATCAACTTTGTATGTTTGATCTTAGAAATGGTTTATGTCACACAGAAGAGAAGTCATATGAC
ATCTCTCATTGTAGTGTTTCAGTACGCTTTTCCGGGTCTTCACTCCCTTATTCTGATTTTCAGCAATCCTAAACTGGAAA
AGGCACTGCTAAAGATTCTT

Alignment

ORF - retro_falb_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.74 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQSNVTSYGTIILAIISLETFAGVWINAFIVCVLCIGWVKKKTLNSNEKILLLLGCSRLSFLCFAWVYSF
          QQSNVTSYGTIILAIISLETFAGVWINAFIVCVLCIGWVKKKT.NSNEKILLLLGC.R...LC..W.YSF
Retrocopy QQSNVTSYGTIILAIISLETFAGVWINAFIVCVLCIGWVKKKTVNSNEKILLLLGCCRFCYLCISWAYSF

Parental  LYIIYPNYLQIQTIYQLLTSLETLFNYSNLYVSACLCVFYCIKIANFRNSFFNYLKVKIDRMVPWVLLAS
          L..IYPNYL...TI.QL.....TLFNYSNL.VSACLCVFYCIKIANFRNSFFNYLKVKIDRMVPW.LL.S
Retrocopy LSRIYPNYLYVHTILQLTVFFQTLFNYSNLWVSACLCVFYCIKIANFRNSFFNYLKVKIDRMVPWLLLGS

Parental  GVSAMAMGIVTYSLNEIVQSNNLTVTCVENFWKATVRMNKHFFIPFFLAGFGYAASFMAVVSSAVLLLFS
          G..A.AMGI..Y.........N.......NF.KA..RM.KHFF..FFLAG.GYAASFMAV...AVLLLFS
Retrocopy GILALAMGIIAYDIADKPHCSNHNSSRQGNFGKASIRMDKHFFPSFFLAGIGYAASFMAVIFAAVLLLFS

Parental  LWKHKCKMQTNSMKDLSVEAHIRAMKSILSFLVMYSINFVCLVSTIIYIMEE-NHVVFLSLLYLYAFPGV
          LWKHKCKMQTNS.KDLSV.AHIRAMKSILSFLVMYSINFVCL.....Y......H...L.....YAFPG.
Retrocopy LWKHKCKMQTNSLKDLSVDAHIRAMKSILSFLVMYSINFVCLILEMVYVTQKRSHMTSLIVVFQYAFPGL

Parental  HSLLLIFSSPKMEKALL
          HSL.LIFS.PK.EKALL
Retrocopy HSLILIFSNPKLEKALL

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_3 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	ENSFALG00000001547	1 retrocopy	retro_falb_3 ,