RetrogeneDB ID: retro_falb_26

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603306.1:489272..490418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIN
• Ensembl ID: ENSFALG00000001842
• Aliases: None
• Description: KIN, antigenic determinant of recA protein homolog (mouse) [Source:HGNC Symbol;Acc:6327]

Sequence

>retro_falb_26
ATGGGGAAGTCGGATTTCCTCAGCCCCAAGGCAATCGCCAACCACATCAAGTCCAAAGGGCTGCAGAAGCTGCCCTGGTG
CTACCAGATGTGCCAAAAGCAGTGCAACAATGAGAATGGCTTCAAGTGTCATTGCACGTCTGAGTCCCACCAGAGGCAGT
TGCTGCTGGCTTCTGAAAATCCTCAGCAATTCATGGATTACTTCTCTGAAAAATTCTGAAATTATTTCATAGAATTGCTC
AGGAGGCGATTTGGAACAAAGAGAGTCTACAATAATATTGTGTACAATAAATACATCAGCCATCAAGAACACATCCACAT
GAATGCCGCACAATGGGACACACTGACTGATTTTACAAAATGGCTGGGGAGAGAAGGTCTTTGCAAGGTTGATGAGACTC
CTAAAGGCTGGTACATTGAGTACATCGACAGGGACCCAGAGACCATTCACAGGCAGCAAGAACAAGAGAGGAAGAAGAAA
CAGGACCTTAATGATGAAAACAAACCTGTTAAATTCATTGAACACATTAGAAGAGAAAGAACTGGAAATGCCAGTCTATA
CTGGACTGAACAGAGAAAACAAGAAAAAATTGCATTTAATTTAAACAAAGGAGGAAACACTTCAGTTGCAGCATCTTCTA
AAACAAGTGTCCTTGGACAGAATGCAGTGAAGATGGTGGAGGGGGCAGTTAAAAGAAAAAGAGCAGCTCATAGTTCTGGT
CAGCCCAAAGAGAAAAAGAAGAAATCTGAACTGGATGAAATCATGGAGCTTGAAGAAAAGAAAAGAACACCTTGAAGAGA
CTACTGATTACAGCCTGAAATCACTGTCAAAATGGTAACAAAAAAGCTTGGAAAGAAGTACCACAAGAAGAAGGCAGTTG
TTAAGAAAGGGACTGACAAGTACACAGCAGCTGTGAAAGTGATTGACTCTGGGGACAAGCTGAAGCTTGATCAAACACAT
CTAGAAACTGTAATACCAGCACCAGGCAATAATGTGATGATGTTAAATGGTGAGTACAGGGGAAATGAAGGTATTTTGGA
ATCCATCACTGAGAAGAGGTTTTCAGTGTCAATAACCATTGACTCGGGACCGTTAAAAGGGTGCAGAGTCAAAGATATCC
AGTATGAAGATGTTTCCAAACTCGCC

Alignment

ORF - retro_falb_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKSDFLSPKAIANRIKSKGLQKLRWYCQMCQKQCRDENGFKCHCMSESHQRQLLLASENPQQFMDYFSE
          MGKSDFLSPKAIAN.IKSKGLQKL.W..QMCQKQC..ENGFKCHC.SESHQRQLLLASENPQQFMDYFSE
Retrocopy MGKSDFLSPKAIANHIKSKGLQKLPWCYQMCQKQCNNENGFKCHCTSESHQRQLLLASENPQQFMDYFSE

Parental  EFRNDFLELLRRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTDFTKWLGREGLCKVDETPKGWYIQ
          .F.N.F.ELLRRRFGTKRV.NNIVYN.YISH.EHIHMNA.QW.TLTDFTKWLGREGLCKVDETPKGWYI.
Retrocopy KF*NYFIELLRRRFGTKRVYNNIVYNKYISHQEHIHMNAAQWDTLTDFTKWLGREGLCKVDETPKGWYIE

Parental  YIDRDPETIRRQQEQERKKKQDLDDEEKTAKFIEQQVRRGLEGKELEMPVYTELNRENEEEKVTFNLSKG
          YIDRDPETI.RQQEQERKKKQDL.DE.K..KFIE...RR...G.......Y....R..E.....FNL.KG
Retrocopy YIDRDPETIHRQQEQERKKKQDLNDENKPVKFIE-HIRRERTG---NASLYWTEQRKQEK--IAFNLNKG

Parental  ASTSVAASSKTSSVLGQNALKMVEGAVKRKEAAHSSGQLKEKKKKSALDEIMELEEEKKRTSRRDYWLQP
          ..TSVAASSKT.SVLGQNA.KMVEGAVKRK.AAHSSGQ.KEKKKKS.LDEIMEL.EEKKRT..RDY.LQP
Retrocopy GNTSVAASSKT-SVLGQNAVKMVEGAVKRKRAAHSSGQPKEKKKKSELDEIMEL-EEKKRTP*RDY*LQP

Parental  EIIVKIVTKKLGEKYHKKKAVVKEVIDKYTAVVKVIDSGDKLKLDQTHLETVIPAPGKKVMVLNGGYRGN
          EI.VK.VTKKLG.KYHKKKAVVK...DKYTA.VKVIDSGDKLKLDQTHLETVIPAPG..VM.LNG.YRGN
Retrocopy EITVKMVTKKLGKKYHKKKAVVKKGTDKYTAAVKVIDSGDKLKLDQTHLETVIPAPGNNVMMLNGEYRGN

Parental  EGILESINEKRFSVTITIDSGPLKGRRVEDIQYEDVSKLA
          EGILESI.EKRFSV.ITIDSGPLKG.RV.DIQYEDVSKLA
Retrocopy EGILESITEKRFSVSITIDSGPLKGCRVKDIQYEDVSKLA

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_26 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26 ,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,