RetrogeneDB ID: retro_falb_7

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603193.1:5707787..5709455(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000015297
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FZD8
• Ensembl ID: ENSFALG00000007019
• Aliases: None
• Description: frizzled family receptor 8 [Source:HGNC Symbol;Acc:4046]

Sequence

>retro_falb_7
GGGGGGGGGGGGGGGGGCTCCAAGGCGCTGGTGTGCCAGGAGATCACGGTGCCGATGTGCAAGGGCATCGGCTACAACCT
CACCTACATGCCCAACCAGTTCAACCACGACACGCAGGACGAGGCCGGGCTGGAGGTGCACCAGTTCTGGCCGCTGGTGG
AGATCCAGTGCTCCCCGGACCTGCGCTTCTTCCTCTGCAGCATGTACACCCCCATCTGCCTGTCCGACTACACGAAGCCG
CTGCCCCCCTGCCGCTCCGTCTGCGAGCGGGCCAAGGCCGGCTGCTCGCCCATCATGCAGCAGTACGGCTTTGCCTGGCC
CGAGAGGATGAGCTGCGACCGCCTGCCGGTGCTGGGGGACTCCGAGGTGCTTTGCATGGGATACAACCACACGGAAGCCA
CCACCCTGCCGCCTTTCTTTGGGAAGCCCACGCGCCCTGCCAAGGACATGGCCAAAAACCTGACGCCTCTCGATGGGCAG
CGCCTCTCGGGGCTGGACTGTGGTCAGACTTGCAAGTGCAAAGCGCCCCTGGTCCCCATCTCCAAGGAGTCCCATCCGCT
GTACAACCGCATCAGGACAGGGAAGGTACTCAACTGCGCCATCCCCTGCTACCAGCCCTACTTCACCCAGGATGAGAAGA
CCTTCGCTACCTTCTGGATCGGCCTCTGGTCCATCCTCTGCTTCCTCTCCACCTCGACCACCGTGGCCACCTTCCTCATT
GACATGGAGCGCTTCAAGTACCCCGAGCGCCCCATCATCTTCCTCTCTGCCTGCTACCTCTTCGTCTCCATGGGCTACAT
TGTGCGCCTGGTGGCAGGGCACGCCAATGTGGCTTGCAGCCCGGAGCACCACCACATCCATTACGAGACCACGGGCCCTG
CTCTCTGCACCGTGGTTTTCCTTCTCCTCTACTTCTTCGGCATGGCCAGCTCCATCTGGTGGGTCATCCTGTCCCTCACC
TGGTTCCTGGCAGCTGGCATGAAGTGGGGCAACGAGGCCATTGCTAGCTACTCGCAGTACTTCCACCTGGCTGCCTGGCT
CATCCCCAGTGCCAAATCCATTGCTGTACTAGCACTGAGCTCTGTGGACGGTGACCCGGTGGCTGGGGTTTGCTACGTGG
GCAACCAGAGCCTGGAGAATCTGCGGGGCTTTGTGCTGGCACCACTAGTGGTTTATCTCTTCACCGGCAGCCTCTTCCTG
CTGGCCGGCTTCGTCTCGCTCTTTCGCATCCGCAGCGTGATCAAGCAGGGCGGCACCAAAACTGACAAGCTGGAGAAGCT
GATGATCCGCATCGGCATCTTCACCGTGCTCTACACTGTGCCTGCCACCATCGTCATTGCCTGCTACATCTACGAGCAGC
ACAACCGGGAGGCCTGGGAGCAGGCACACAACTGCTCCTGCCCGGGGGACCCTCAGCGCCCCAAGCCTGACTATGCTGTC
TTCATGCTCAAGTACTTCATGTGCCTCGTGGTGGGGATCACCTCCGGCGTTTGGATCTGGTCTGGCAAGACCCTGGAGTC
CTGGCGGCGCTTCGGCACGCGCTGCTGCCGGGCCAGGAAGCCTGCGGGCGCCTCTGTGTACGGTGAGGCCAGCCCGGCGC
TGGTGGGCAGGACGGTGCTGCCCAGTATGGCCTCCTACCACAAGCAGGTCCCACTGTCCCATGTGTGA

Alignment

ORF - retro_falb_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.57 %
• Parental protein coverage: 92.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKELSCQEITVPLCKGIGYNYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSSDLRFFLCSMYTPICLED
          .K.L.CQEITVP.CKGIGYN.TYMPNQFNHDTQDEAGLEVHQFWPLVEIQCS.DLRFFLCSMYTPICL.D
Retrocopy SKALVCQEITVPMCKGIGYNLTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLRFFLCSMYTPICLSD

Parental  YKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQGSPDTLCMDYNRTDLTTAAP---PPAKP
          Y.KPLPPCRSVCERAKAGC.P.M.QYGFAWP.RM.CDRLP..G....LCM.YN.T..TT..P....P..P
Retrocopy YTKPLPPCRSVCERAKAGCSPIMQQYGFAWPERMSCDRLPVLGDSEVLCMGYNHTEATTLPPFFGKPTRP

Parental  PLRGSKPGTPARGG--GGGGGGPGCQCRAPMVSVSSERHPLYNRVKTGQIANCALPCHNPYFSPDERAFT
          .....K..TP..G....G...G..C.C.AP.V..S.E.HPLYNR..TG...NCA.PC..PYF..DE..F.
Retrocopy AKDMAKNLTPLDGQRLSGLDCGQTCKCKAPLVPISKESHPLYNRIRTGKVLNCAIPCYQPYFTQDEKTFA

Parental  AFWIGLWSVLCFLSTFATVSTFLIDMERFKYPERPIIFLAACYLFVSLGYLVRLVAGRGELAVA---EHV
          .FWIGLWS.LCFLST..TV.TFLIDMERFKYPERPIIFL.ACYLFVS.GY.VRLVAG....A......H.
Retrocopy TFWIGLWSILCFLSTSTTVATFLIDMERFKYPERPIIFLSACYLFVSMGYIVRLVAGHANVACSPEHHHI

Parental  RYESTGPALCTVVFLLVYFFGMASSIWWVILSLTWFLAAGMKWGNEAIAGYAQYFHLAAWLLPSVKSIAV
          .YE.TGPALCTVVFLL.YFFGMASSIWWVILSLTWFLAAGMKWGNEAIA.Y.QYFHLAAWL.PS.KSIAV
Retrocopy HYETTGPALCTVVFLLLYFFGMASSIWWVILSLTWFLAAGMKWGNEAIASYSQYFHLAAWLIPSAKSIAV

Parental  LALSSVDGDPVAGICYVGNQSLENLRGFVLAPLLIYLAIGSMFLLAGFVSLFRIRSVIKQQGGPTKTHKL
          LALSSVDGDPVAG.CYVGNQSLENLRGFVLAPL..YL..GS.FLLAGFVSLFRIRSVIKQ..G.TKT.KL
Retrocopy LALSSVDGDPVAGVCYVGNQSLENLRGFVLAPLVVYLFTGSLFLLAGFVSLFRIRSVIKQ--GGTKTDKL

Parental  EKLMIRLGLFTVLYTVPAASVVACLFYEQHNRPRWEATHNCPCLRDQQPDQARRPDYAVFMLKYFMCLVV
          EKLMIR.G.FTVLYTVPA..V.AC..YEQHNR..WE..HNC.C..D.Q......PDYAVFMLKYFMCLVV
Retrocopy EKLMIRIGIFTVLYTVPATIVIACYIYEQHNREAWEQAHNCSCPGDPQ---RPKPDYAVFMLKYFMCLVV

Parental  GITSGVWVWSGKTLESWRALCTRCCWASK
          GITSGVW.WSGKTLESWR...TRCC.A.K
Retrocopy GITSGVWIWSGKTLESWRRFGTRCCRARK

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_7 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001137	1 retrocopy	retro_acar_5,
Callithrix jacchus	ENSCJAG00000014119	1 retrocopy	retro_cjac_213,
Ficedula albicollis	ENSFALG00000007019	1 retrocopy	retro_falb_7 ,
Petromyzon marinus	ENSPMAG00000005873	1 retrocopy	retro_pmar_8,