RetrogeneDB ID: retro_falb_5

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603184.1:10720282..10721122(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014998
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000000023
• Aliases: None
• Description: None

Sequence

>retro_falb_5
ATGGCTCGCAGTGCAGAGAAGGCTGTGACAGCCTTGGCGAGATTTCGGCAAGCCCAGCTTGAGGAAGGGAAAGCCAAGGA
GAGAAGGCCTTTCCTTGCCTCAGAGTGTAATGAGCTGCCCAAAGCTGAGAAATGGAGGAGACAGATAACTGGGGAGATTT
CTAAGAAAGTGGCACCGATCCAAAATGCTGGATTGGGTGAATTCAGAATTCGGGACCTGAATGATGAAATAAACAAACTT
CTGAGAGAGAAGGGACACCGGGAATACAGAATAAGGGAGCTGGGAGGTCCTGATTATGCTAGAATTGGCCCAAAAATGTT
AGATCATGAAGGGAAAGAAGTTCCAGGAAACAGAGGCTACAAATACTTTGGGGCTGCAAAGGACTTGCCAGGAGTTAGAG
AGCTTTTTGAAAAGGAACCCCTGCCACCCCCATGGAAGGCTCTGGCTGAGCTTATGAAGGACATCGATGCTGAGTACTAT
GTTTACAGGGATGAAGATGATGGGATTCTGGAGCCCCTGGAGCAGGAATATGAGAAGAATGTTATAGCAGAAGCAGTGGA
AAAATGGAAGATGGAGAGAGAAGCACGACTTGCAAGAGGTGAGGAGGAGGAGGAAGAAAACATCTATGCTGACCATGGGG
AACAATCTGATGAGGAAGGTGGCAAGGAGAGAGGAGGTGAAGATGGCCAACAGAAATTTACTGCACATGTTCCAGTGCCA
ACTCAGCAGGAGATTGAGGAGGCTCTTGTAAGAAGAAAGAAGCTGGAGCTGCTCCAGAAGTACGCCAGTGAAACCCTCCT
GGCACAGAGTGAGGAGGCAAAGACACTTATAGCATTTTAA

Alignment

ORF - retro_falb_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARNAEKAMTALARFRQAQLEEGKVKERRPFLASECNELPKAEKWRRQIIGEISKKVAQIQNAGLGEFRI
          MAR.AEKA.TALARFRQAQLEEGK.KERRPFLASECNELPKAEKWRRQI.GEISKKVA.IQNAGLGEFRI
Retrocopy MARSAEKAVTALARFRQAQLEEGKAKERRPFLASECNELPKAEKWRRQITGEISKKVAPIQNAGLGEFRI

Parental  RDLNDEINKLLREKGHWEYRIKELGGPDYARIGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVRELFEKEP
          RDLNDEINKLLREKGH.EYRI.ELGGPDYARIGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVRELFEKEP
Retrocopy RDLNDEINKLLREKGHREYRIRELGGPDYARIGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVRELFEKEP

Parental  LPPPRKTRAELMKDIDAEYYGYRDEDDGILEPLEQEHEKKVIAEAVEKWKMEREARLARGEEEEEENIYA
          LPPP.K..AELMKDIDAEYY.YRDEDDGILEPLEQE.EK.VIAEAVEKWKMEREARLARGEEEEEENIYA
Retrocopy LPPPWKALAELMKDIDAEYYVYRDEDDGILEPLEQEYEKNVIAEAVEKWKMEREARLARGEEEEEENIYA

Parental  VHEEESDEEGGKEREGEDGQQKFIAHVPVPTQQEIEEALVRRKKMELLQKYASETLLAQSEEAKTLL
          .H.E.SDEEGGKER.GEDGQQKF.AHVPVPTQQEIEEALVRRKK.ELLQKYASETLLAQSEEAKTL.
Retrocopy DHGEQSDEEGGKERGGEDGQQKFTAHVPVPTQQEIEEALVRRKKLELLQKYASETLLAQSEEAKTLI

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_5 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006886	1 retrocopy	retro_dord_331,
Ficedula albicollis	ENSFALG00000000023	1 retrocopy	retro_falb_5 ,
Loxodonta africana	ENSLAFG00000004015	2 retrocopies	retro_lafr_1070, retro_lafr_1170,
Myotis lucifugus	ENSMLUG00000011804	1 retrocopy	retro_mluc_1401,
Oryctolagus cuniculus	ENSOCUG00000003923	1 retrocopy	retro_ocun_1485,