RetrogeneDB ID: retro_falb_1

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: AGTO01003143.1:307..3115(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000015332
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000012537
• Aliases: None
• Description: None

Sequence

>retro_falb_1
TCCTCCACAGCCATGGCCTCGCCAGAGGACACACAAGAGGGGGATGCAAAGGCACAGCTCCTGGCAGAGGCATTTCAGAA
GGAAGGACTGGATGCTGGATACTGGCTGCCCAAAATGTCACAGATCCTGGGAATCAAGTGCAGAGAAGCCCTGCAGCATC
TGGAATATAAAGACTACCTCAAGCTGGAGTGTGAGGTACGGCACCCCTGGGAGAAAAAGGCACTCCAGAAACTCCTGAAT
ATAACAGATGACAAAACAGCCTCTAAAGAGGTGCAAAAGGAGCACATGGAGAAGGCAAAGCAAAGGCAGGAAGTGGCCAA
ACAAGCCCTGAAAGATCTGACAGAAATGCTCAACAGCCACAGCCACAGCCAGGATGTGCTGAGGGAGCAAGCAGAGACTC
TGTGGCAAGCCATGGAGATTCCCAAAGAGTTCTGGCCATCGCCAAAGGAACCCTTGGCAGAAATGCTGGAGAGCATCCAT
AAGCAGCTGGAGCAGCAGCAGGAGATGTCAGCAGGCAGGAGGGAGAACATCCCTGACACCGAGGTGCTGAGGCGGGCGTC
GGGGGGACTGGCCCTGCAGGGCATCTACAGAACCAGCAGAGCTGGAGATGTGCTGGCAACGCGAGAGCAGCTCCTCAGGG
TTCCTGAGGGATTCCAGCTCGCCGGTCCAGAGCAAGGATCAATGCTTGAGAGGAGGGAGTTCTCCTCCTCTGCAGCAGAA
TCCACTTTCACCAAGTCCATGGAGCAGCTGGGGTTCAGCATGAGCATTTCTACCAAATTTGCATTCTGGAAAGTTAATCC
GGGAGCGGTTGTAGATCACAGCAGCTCCTCGCAGTCCGACGCCACCCACCAGTGCCACTCTGAGCAGAGCTACTTCTGCA
CCACCAAGTTCCAGTACATCCCCCTGGCCTCCTGCTACTTCCAAAGGCATCAGCTTTGCCTCTCGGATGCGGCTCTGCGG
GAGCTGCAAGACATGGAGCAGATTTTGGGCTTCACTCGGAAAGAGGACAACCCAGACTTTGTGAAAATGTGTGAGAGCTT
CTTCAGCAGGTTTGGATCCCACATAAACCAGGGTCCCCTCCACTTTGGGGGGATATTCTGGTGGAAGGCGTCCACAGAAG
GATTCCAAGCTGAGCAACAGGAAGAGGTGAAGCGACAAACATCTGCAGCACTGAACAGCTTTGTCAGGAAGAGCTATGGT
GACTTCCCCGCAAGTGCTGCAGGGGCCCTGGATGTTTCCAAATCCATCTCACAGGCTTCTGTCCTGGGAAGAACCGGAGA
GAATTCCCATTCAGCCATTCAGCTCTCTGTGATCAACACAGGGGGCCCAGCAGACACAACTTCTCTTCCTCAGTGGAAAA
CGGGGCTCGTGTCTGATAACACAACGTGGTGCGTTATCGACCGTGGCTTTGAGCTGATCCCAGTGTGGGACGTCATCCTG
TGCAATCACAGTGGGGATTTTAAGTCTATTGATCAGATGAGCGGAGCCCTCAGGGATGCGTACAAAGCGCTGACGAATGA
GAGTGTTGGAACCATTTTTGGAGAGGACCTGGGCAGTGCAGTGCAAGAGGCCAGAGATTTCATGGAGACTGTGAAGGCCT
GGGAGGTACCAGCGGATGAAAGGAAGCTGCTCCTGCTGATGGAGCTCAAAGATGATCTGAATGCAAAAACCAGGAACCAC
AGTGTGTGGATCAATGTGTGCCTGTCAGACAAAGCCCTGCAGGACTTCCTGGTGAACACTGTGTGGAGCTACAAGGAGTC
ACCTCCAGAAAGCACCTCCTCTGTCAAGGTAATGCTGAGAAGCCTCCTGGATCCTCACATCTACTCTGTCAAGGACTTCC
CTGAGGCTTCTTTCATTATGCAATGGATCTTCCAGACTGAGCACCAGCTTCCCGTATCTCCCAAAATCTCTGAGCTTGAA
GAACTCATCAAAACACTGAAGCAAATGAAGGAGCACATCTATGCTGTCACCTACGCACCAGGAAGCTCTGCTTCTGCCGT
TCATGAAGCAAAGATAAAAGCCACCCTGACCAGCAGCCTCGCCATTTATTCCTTACTCCAGTCTCTCCAGGAACGGGCTG
AGAAGGACATGGAACTGTTGGTGCTCTTGATTGTGACCAGCACAGGGTACCAGGTGGAAAGCAGCACTTTTCAGCACCTC
CTTGGACATCCAGAAATTCTGTACATGGCCAAGGAAATGGCAGAGGCATATGAGGAGTACGTGAACCTGAAGGAGCAGGA
TGCTGACACAGCTGAGGCCTCCCTTCTGCTGATGGGTCTGACTGTGACACCAGAAAGTCAAAAGCTGTCCCCTGAGCAGA
AGAGGGAGCGTTTAGTTTTCATGGAGGATCACATGAAAGGCTTGTGGTCCACACGGATAAAGAATCTCCTCCGAAAGCAC
AGTGCAGATGGAGACTGGGAGAGGCTGGAACAGGACTTGAATTCCTTGATCAGTGGGTGCTTGGATGACAAACTGGACAA
AAAGAAGATGCACAACATACTCACAGACCTGGAAGACACTTTTGCAAAATCTGAGGCACCCAGTGAGTCTCAACCAAAGC
CAGACAGCAGCCAATCCAAAGCAAATGAAGCCATTGCAAACCAGGAATTCCTCCAGTTGCTCAAGCGCCTTGGACTTGAA
AGTCACTATCCAAGAAAAATGGGGATGGGAGATTTCTGCACCATTTGCAGAACATCTCTGCAGGACAGCCAGCCCAGCAA
GGACAAGGAACTGCCCTTCTACTTCTTGCAAAAGCTCTTAACTGTGGATTACCAGGTGAGGTACTTGACTTGCTGGGAAA
CAAGCAGC

Alignment

ORF - retro_falb_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 74.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSTAMASQEDTQEGDAKAQLLAEAFQKEGLDAGYWLPKMSQILGIKCREALQHLEYEDYLKLECAARHPW
          SSTAMAS.EDTQEGDAKAQLLAEAFQKEGLDAGYWLPKMSQILGIKCREALQHLEY.DYLKLEC..RHPW
Retrocopy SSTAMASPEDTQEGDAKAQLLAEAFQKEGLDAGYWLPKMSQILGIKCREALQHLEYKDYLKLECEVRHPW

Parental  EKKALKKLLNITDDKTASKEVQKEHLEKTKQRQEVAKQALKDLTEMLNSHSHSQDVLREQTETLWRAMEI
          EKKAL.KLLNITDDKTASKEVQKEH.EK.KQRQEVAKQALKDLTEMLNSHSHSQDVLREQ.ETLW.AMEI
Retrocopy EKKALQKLLNITDDKTASKEVQKEHMEKAKQRQEVAKQALKDLTEMLNSHSHSQDVLREQAETLWQAMEI

Parental  PKEFWPSPKEPLAEMLESIHKQLEQQQEMSAGRRENIPDTEVLRRASGGLALQGIYRTSRAGDVLATREQ
          PKEFWPSPKEPLAEMLESIHKQLEQQQEMSAGRRENIPDTEVLRRASGGLALQGIYRTSRAGDVLATREQ
Retrocopy PKEFWPSPKEPLAEMLESIHKQLEQQQEMSAGRRENIPDTEVLRRASGGLALQGIYRTSRAGDVLATREQ

Parental  LLRVPEGFQLAGPKQGSQLDSREFSSSAEESNFTMSMEQLGFSMRFSAKFFTLWGINLKDSVDYSRSSQS
          LLRVPEGFQLAGP.QGS.L..REFSSSA.ES.FT.SMEQLGFSM..S.KF...W..N....VD.S.SSQS
Retrocopy LLRVPEGFQLAGPEQGSMLERREFSSSAAESTFTKSMEQLGFSMSISTKF-AFWKVNPGAVVDHSSSSQS

Parental  EATHQSYSEQSYFCTTKFQYIPLASCYFQRHQLHLSDAALRELQHMEQIMGFTQNEDNPIILLQEMCESF
          .ATHQ..SEQSYFCTTKFQYIPLASCYFQRHQL.LSDAALRELQ.MEQI.GFT..EDNP......MCESF
Retrocopy DATHQCHSEQSYFCTTKFQYIPLASCYFQRHQLCLSDAALRELQDMEQILGFTRKEDNPDFV--KMCESF

Parental  FSRFGSHINQGPLHFGGIFWWKASTKGFRAEQREKVKRQTSEALNSFVRKSYGDVLESAAGALDVSTSSS
          FSRFGSHINQGPLHFGGIFWWKAST.GF.AEQ.E.VKRQTS.ALNSFVRKSYGD...SAAGALDVS.S.S
Retrocopy FSRFGSHINQGPLHFGGIFWWKASTEGFQAEQQEEVKRQTSAALNSFVRKSYGDFPASAAGALDVSKSIS

Parental  KASVLRRAAESSHTAIQFYVANTGGPADTTSLPQWKTGLVSDNTTWCVIDRGFELIPVWDVILCNHSGDF
          .ASVL.R..E.SH.AIQ..V.NTGGPADTTSLPQWKTGLVSDNTTWCVIDRGFELIPVWDVILCNHSGDF
Retrocopy QASVLGRTGENSHSAIQLSVINTGGPADTTSLPQWKTGLVSDNTTWCVIDRGFELIPVWDVILCNHSGDF

Parental  KSVGQMSRALRDAYKALTNESVGEIFGEELDSAVQEARDFMETVKAWEVTVDERKLHMLMEVKDDLSAKT
          KS..QMS.ALRDAYKALTNESVG.IFGE.L.SAVQEARDFMETVKAWEV..DERKL..LME.KDDL.AKT
Retrocopy KSIDQMSGALRDAYKALTNESVGTIFGEDLGSAVQEARDFMETVKAWEVPADERKLLLLMELKDDLNAKT

Parental  KNHRVWTNVCLSDRALQDFLVNTVRSCQESPPESTSSIKVMLRSLLDPHIYFVKDFPEASFIMKWIFQNE
          .NH.VW.NVCLSD.ALQDFLVNTV.S..ESPPESTSS.KVMLRSLLDPHIY.VKDFPEASFIM.WIFQ.E
Retrocopy RNHSVWINVCLSDKALQDFLVNTVWSYKESPPESTSSVKVMLRSLLDPHIYSVKDFPEASFIMQWIFQTE

Parental  HPLPRSPKISELEELIKTLQEMKEHIYAVTYAP
          H.LP.SPKISELEELIKTL..MKEHIYAVTYAP
Retrocopy HQLPVSPKISELEELIKTLKQMKEHIYAVTYAP

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_1 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	ENSFALG00000012537	1 retrocopy	retro_falb_1 ,