RetrogeneDB ID: retro_falb_12

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603341.1:70358..71567(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014860
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000013473
• Aliases: None
• Description: None

Sequence

>retro_falb_12
ATGAGCCAAGATATTCTAGTGAACACCCTTCCTACAGAAGGGGCAAATTATCTGAGCCTGGAGGAGCCAAAGAAGATGAT
GAGGGAAAACTGGAGGAAAAAGAAAGAGTTGGAAGAACAGAGAAAACTAGGAAATGCACCTGCTGAAGTGGTTGAAGAAG
GAAAAGATATCAACCCTCATATTCCTCAGTACATCTCCTCAGTGCCATGGTACATAGATCCTTCTAGAAGACCCACGCTA
AAGCATCAGAGACGTCAGCCAGAGAAGCAGAAACAGTATAGCTCCTCTGGAGATTGGTACAAACGAGGACTGCAGGAGCA
CAGCGTGGCCACGAGGTACCGTAAAGGAGCCTGTGAGAACTGTGGGGCACTGACACACAAAAGGAAAGACTGCATGGAGA
GACCCAGGAAAGCTGGAGCAAAATACACAGGCATGAATATTGCCCCAGATGAACATGTGCAGCCTCAGCTGATGTTTGCT
TATGATGGGAAGCGAGACCGATGGAATGGTTATAACCCAGAGGAGCACATGAAAACTGTCAAGAAGTATTCCAAGGTTGA
TTTGGCCAAACGTACACTGAAAGCTCAGAAGCTTCAGGAGGAGTTGGCATCAGAGAAGCTGGAGCAAGTTAACTCCCCAA
AACACCAGTGGGGAGAAGAGGAATCAAATTCACAGACAGAAAGAGATCATAACAGTGAAGATGAAGACAAATATGCAGGT
GATATTGATACGCCTGGGCAGAACTTTGACTCTAAAAGACGCATCACAGTCCGAAATTTACGTATTCGGGAAGATACTGC
AAAATACTTAAGGAATCTAGATCCAAACTCTGCTTATTATGATCCCAAAACAAGAGCAATGAGGGAGAACCCTTATGCCA
ACATAGGCAAGGATCTAGATGAAGTTAGTTATGCAGGTGACAACTTCATTCGTTACACAGGCAATACCATTTCAATGGCT
CAGGCTCAGTTGTTTGCCTGGGAGGCTTATGACAAAGGCTCTGAAGTTCATCTTCAAGCAGACCCTACAAAATTAGAGCT
CCTTTATAAATCGTTCAAAGTGAAAAAAGAAGATTTCAAGGCACAGCAGAAAGAAAGCATCCTAGAGAAGTATGGAAGAC
AAGAACATTTAGATGCCTCTCCCCCCCGCCCAGCTGAACTGCTGTTAGTTCAAACAGAAGATTATTTGGAGACAATGGCA
CCCCCTGAG

Alignment

ORF - retro_falb_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 68.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGAVANAPPAGGTNDVSLEEPKKMTREDWRKKKELEEQRKLGNAPAEVDEEGKDINPHIPQYISSVPW
          M......N..P..G.N..SLEEPKKM.RE.WRKKKELEEQRKLGNAPAEV.EEGKDINPHIPQYISSVPW
Retrocopy MSQDILVNTLPTEGANYLSLEEPKKMMRENWRKKKELEEQRKLGNAPAEVVEEGKDINPHIPQYISSVPW

Parental  YIDPSKRPTLKHQRPQPEKQKQYNSSGDWYKRGVQEHAVATRYRKGACENCGALTHKKKDCMERPRKVGA
          YIDPS.RPTLKHQR.QPEKQKQY.SSGDWYKRG.QEH.VATRYRKGACENCGALTHK.KDCMERPRK.GA
Retrocopy YIDPSRRPTLKHQRRQPEKQKQYSSSGDWYKRGLQEHSVATRYRKGACENCGALTHKRKDCMERPRKAGA

Parental  KYTGMNIAPDEHVQPQLMFDYDGKRDRWNGYNPEEHMKIVEEYSKVDLAKRTLKAQKLQEELASGKLEQV
          KYTGMNIAPDEHVQPQLMF.YDGKRDRWNGYNPEEHMK.V..YSKVDLAKRTLKAQKLQEELAS.KLEQV
Retrocopy KYTGMNIAPDEHVQPQLMFAYDGKRDRWNGYNPEEHMKTVKKYSKVDLAKRTLKAQKLQEELASEKLEQV

Parental  NSPRHQWGEEESNSQTERDHNSEDEDEDKYADDIDMPGQNFDSKRRITVRNLRIREDIAKYLRNLDPNSA
          NSP.HQWGEEESNSQTERDHNS..EDEDKYA.DID.PGQNFDSKRRITVRNLRIRED.AKYLRNLDPNSA
Retrocopy NSPKHQWGEEESNSQTERDHNS--EDEDKYAGDIDTPGQNFDSKRRITVRNLRIREDTAKYLRNLDPNSA

Parental  YYDPKTRAMRENPYANTGKNPDEVGYAGDNFVRYTGDTISMAQTQLFAWEAYDKGSEVHLQADPTKLELL
          YYDPKTRAMRENPYAN.GK..DEV.YAGDNF.RYTG.TISMAQ.QLFAWEAYDKGSEVHLQADPTKLELL
Retrocopy YYDPKTRAMRENPYANIGKDLDEVSYAGDNFIRYTGNTISMAQAQLFAWEAYDKGSEVHLQADPTKLELL

Parental  YKSFKVKKEDFKAQQKESILEKYGGQEHLDAPP---AELLLAQTEDYVE
          YKSFKVKKEDFKAQQKESILEKYG.QEHLDA.P...AELLL.QTEDY.E
Retrocopy YKSFKVKKEDFKAQQKESILEKYGRQEHLDASPPRPAELLLVQTEDYLE

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_12 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004484	1 retrocopy	retro_cpor_883,
Dipodomys ordii	ENSDORG00000006239	3 retrocopies	retro_dord_125, retro_dord_140, retro_dord_563,
Ficedula albicollis	ENSFALG00000013473	1 retrocopy	retro_falb_12 ,
Myotis lucifugus	ENSMLUG00000003091	2 retrocopies	retro_mluc_2250, retro_mluc_2251,
Oryctolagus cuniculus	ENSOCUG00000011743	1 retrocopy	retro_ocun_818,
Otolemur garnettii	ENSOGAG00000012301	1 retrocopy	retro_ogar_1519,
Sorex araneus	ENSSARG00000012209	2 retrocopies	retro_sara_409, retro_sara_731,