RetrogeneDB ID: retro_falb_22

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603203.1:7027754..7028378(-)
• Located in intron of: ENSFALG00000004391

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM45
• Ensembl ID: ENSFALG00000003330
• Aliases: None
• Description: RNA binding motif protein 45 [Source:HGNC Symbol;Acc:24468]

Sequence

>retro_falb_22
TTTATTGCACAGGCTGGAAGCCACCAAGATATTGAAGATGAGGAGCTCACACAAATCTTGGTTATGATACCAAAAACCTG
CACGGAGGAGGATCTGTGAGAGAAGTGTAAGATGTGTGGAGACATTGAATGCTGCAGCAGAATTAAGAGCAGGACTACTG
GAGCAAGTAAAGGTTTGGGCTGTGTCAGGTACCTGAAACCATGACAAGCTGCCCCAGCCATTGAACAATGTGATCAAAGC
TACAAGGCCATTTTGGCCGAACCTAAAAATAAGTCATTGAGTCTTCTGAACACAATTACCACAGTAATAGCATGAGTCCA
GAATTAAGAGGAAATACACTTCCATTTTGTATGCAGCCAGAATTTTGTAGCTTTGAAAAAGCTGAGACCCAATTCAAGAA
CCAGTCTCCCAGCACCTGTCAGTGGTATCTCAGCTGCCCTTTCACCAAGAGCAGCTGTCAGCCCTCTTCAATTCAGTTCC
AGGTCTGGAATATTGTGATGTCCAGCAAGACCCTCATGCCAACAGTGGGTACACTGTGACTTGGTACAGCTCTGCTGCTT
CTGCTGAACCTGCCAAGAACAAACTACATGGGTTTAGTGTCCTCCTGGAAATCAACTGCCAGTT

Alignment

ORF - retro_falb_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.49 %
• Parental protein coverage: 56.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FIAQSRASGSHRDLEDEELTRIFVMIPKTYTEEDLREKFKMYGDIEYCSIIKNKTTGESKGLGYVRYLKP
          FIAQ....GSH.D.EDEELT.I.VMIPKT.TEEDL.EK.KM.GDIE.CS.IK..TTG.SKGLG.VRYLKP
Retrocopy FIAQA---GSHQDIEDEELTQILVMIPKTCTEEDL*EKCKMCGDIECCSRIKSRTTGASKGLGCVRYLKP

Parental  SQAALAIEECDRSYRAILAEPKNKS-SESFEHDYYCNSMRPELRGNTLPFCMQPEFCSFEKAETR-VQEP
          .QAA.AIE.CD.SY.AILAEPKNKS..ES.EH.Y..NSM.PELRGNTLPFCMQPEFCSFEKAET...QEP
Retrocopy *QAAPAIEQCDQSYKAILAEPKNKS<IESSEHNYHSNSMSPELRGNTLPFCMQPEFCSFEKAETQ<IQEP

Parental  VSKRLSVISRLPFIQEQLFALFDLIPGLEYCDVQRDPHTNSGYAVIQYSTAASAIYAKYKLHGFEY-PSG
          VS..LSV.S.LPF.QEQL.ALF...PGLEYCDVQ.DPH.NSGY.V..YS.AASA..AK.KLHGF...P.G
Retrocopy VSQHLSVVSQLPFHQEQLSALFNSVPGLEYCDVQQDPHANSGYTVTWYSSAASAEPAKNKLHGFSV<PPG

Parental  NRLTV
          N.L.V
Retrocopy NQLPV

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_22 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000003330	2 retrocopies	retro_falb_21, retro_falb_22 ,