RetrogeneDB ID: retro_falb_9

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603209.1:1615910..1616510(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFALG00000014244
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFALG00000008988
• Aliases: None
• Description: None

Sequence

>retro_falb_9
ATGGCGTCAGGCAGCGGCACCAAGAACCTGGACTTCCGCCGGAAATGGGACAAGGATGAATACGAGAAACTCGCAGAGAA
GTGGCTCGCAGAGGAGAGAGAAAAGAAACACGGCAAACCAGCTCAGCCTGTCAAAAGGGAACTTCTGCAGCACCGAGGCT
ACAAAGTGGACCTGGAATCCAAGCTGGGCAAAACCATTTTCATCACCAAAACTACCCCTCAGTCAGAGATGGGAGGGTAT
TACTGTAACATATGTGACTGTGTGGTGAAAGATTCCATTAACTTCTTGGATCACATCAATGGCAAAAAACACCAGAGGAA
TCTGGGCATGTCCATGCGGGTGGAGCGCTCTACACTGGAGCAGGTGAAGAAACGCTTTGAGGTGAATAAGAAGAAGATGC
AGGAGAAGAAGAAGGAGTATGACTTTGAGGAGAGGATGAAGGAACTCCGTGAGGAGGAGGAGAAGGTCAAAGCCTACAAG
AAGAAGATGCAGAGAGAGAAGAAGAGGCAGGTGGAGGAAGATTTGACCTTCGAAGAAAACCATGAAATGGCAGCTGTGAT
GGGTTTCTCTGGTTTCAGCTCAACCAAAAAGAATCACTGA

Alignment

ORF - retro_falb_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPAQPVKRELLRHRDYKVDLESKLGKTIVITKTTPQ
          S.TKNLDFRRKWDKDEYEKLAEK.L.EEREKK.GKPAQPVKRELL.HR.YKVDLESKLGKTI.ITKTTPQ
Retrocopy SGTKNLDFRRKWDKDEYEKLAEKWLAEEREKKHGKPAQPVKRELLQHRGYKVDLESKLGKTIFITKTTPQ

Parental  SEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLDQVKKRFEVNKKKMEEKQKDYDFEE
          SEMGGYYCN.CDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTL.QVKKRFEVNKKKM.EK.K.YDFEE
Retrocopy SEMGGYYCNICDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLEQVKKRFEVNKKKMQEKKKEYDFEE

Parental  RMKELREEEEKAKAYKKEKQREKKRRAEEDLTFEEDDEMAAVMGFSGFGSTKKSH
          RMKELREEEEK.KAYKK..QREKKR..EEDLTFEE..EMAAVMGFSGF.STKK.H
Retrocopy RMKELREEEEKVKAYKKKMQREKKRQVEEDLTFEENHEMAAVMGFSGFSSTKKNH

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_9 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005907	1 retrocopy	retro_cfam_822,
Choloepus hoffmanni	ENSCHOG00000007795	2 retrocopies	retro_chof_101, retro_chof_514,
Callithrix jacchus	ENSCJAG00000016231	3 retrocopies	retro_cjac_1137, retro_cjac_1472, retro_cjac_4007,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133, retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9 ,
Myotis lucifugus	ENSMLUG00000017525	2 retrocopies	retro_mluc_2281, retro_mluc_2309,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209,
Pteropus vampyrus	ENSPVAG00000009717	1 retrocopy	retro_pvam_827,
Ictidomys tridecemlineatus	ENSSTOG00000002025	1 retrocopy	retro_itri_1272,
Tursiops truncatus	ENSTTRG00000001777	4 retrocopies	retro_ttru_1889, retro_ttru_340, retro_ttru_721, retro_ttru_766,