RetrogeneDB ID: retro_falb_23

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: JH603216.1:5677935..5678693(+)
• Located in intron of: ENSFALG00000004193

Retrocopy information

• Ensembl ID: ENSFALG00000004194
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAP30BP
• Ensembl ID: ENSFALG00000001071
• Aliases: None
• Description: SAP30 binding protein [Source:HGNC Symbol;Acc:30785]

Sequence

>retro_falb_23
AGGGGGGCAGCACAGCAGAGTTCTCTCCTCGCCGGCGGCGCACGGCCGGGACTCGGAGCTGCAGCCGGACAGCCAGGACA
AAGTGTCCCCTGGAGCAGCACGGGACAGGAAGGGGGCCTGGTGTCACCCGGGTATGGAGAGGATGGCTTTACCTGCCTGG
GTGGCCATGAGGAAGGCTACAAAGAGGAGGATGGTGGGAACAGCAGGCAGTCAGATGGAGATTCACAGACCGAAAAACCT
GAGGCTGGTGACCTAAAGGAATTCCGAGAAGTGGAGGAAAGAGATCCTCAAGAACTGGTTGCCTCTTTTTCAGAGAGAGT
GCAGAAGATGTCTCCAGATGAGATCAAAATCCCTCCTGAGCCTCCTGGCAGATGTTCTAACCAACTGCAGGATAAAATTG
AGAAGCTGTATAGAGGAAAAGGAAAGAGGGCATGGATATGAACAGCATCATCCAGAAGAAAAAGGCATTTCGCAACCCCA
GCATCTACGAAAAGCTGATCCAGTTTTGTTCCACTGATGAATTTGGTACAAATTACCCAAAGGACATGTTTGATCCTCAC
AGCTGGTCAGAGGATTCATATTATGAGGCACTAGCTAAAGCCCAGAAGATTGAGATGGACAAATGGAAGAAGGCCAAGAA
AGAATGTACAAAGATTGAATTTGTGACTGGCACTAAAAAAGGTACAACAAGCGCTGCTTCCACAACCACCACGACATCCA
GCACCAGTGTGGGAGATGCCCAGAGGAAGAGGAGGAGG

Alignment

ORF - retro_falb_23 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.22 %
• Parental protein coverage: 81.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSVLSSLAVYAEDSDPESDSEAGTAG-SDGGAAAGEKGGLVSVGYGEDDFSRVDGDEEGYEEEDDENSRQ
          R.........A....P.....AG..G.S......G..GGLVS.GYGED.F....G.EEGY.EED..NSRQ
Retrocopy RGAAQQSSLLAGGARPGLGAAAGQPGQSVPWSSTGQEGGLVSPGYGEDGFTCLGGHEEGYKEEDGGNSRQ

Parental  SEDDDSETEKPEAGDLKEFSEVEKRDPQELVASFSERVRNMSPDEIKIPPEPPGRCSNQLQDKIQKLYE-
          S.D.DS.TEKPEAGDLKEF.EVE.RDPQELVASFSERV..MSPDEIKIPPEPPGRCSNQLQDKI.KLY..
Retrocopy S-DGDSQTEKPEAGDLKEFREVEERDPQELVASFSERVQKMSPDEIKIPPEPPGRCSNQLQDKIEKLYR<

Parental  RKVKEGMDMNYIIQRKKEFRNPSIYEKLIQFCSIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKIEMDK
          RK.KEGMDMN.IIQ.KK.FRNPSIYEKLIQFCS.DE.GTNYPKDMFDPH.WSEDSYYEALAKAQKIEMDK
Retrocopy RKRKEGMDMNSIIQKKKAFRNPSIYEKLIQFCSTDEFGTNYPKDMFDPHSWSEDSYYEALAKAQKIEMDK

Parental  LEKAKKERTKIEFVTGTKKGTTTSAASTTTTTSSTTVGDAQKRKSK
          ..KAKKE.TKIEFVTGTKKG.TTSAASTTTTTSST.VGDAQ.....
Retrocopy WKKAKKECTKIEFVTGTKKG-TTSAASTTTTTSSTSVGDAQRKRRR

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_23 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000001071	1 retrocopy	retro_falb_23 ,
Macropus eugenii	ENSMEUG00000013106	2 retrocopies	retro_meug_1388, retro_meug_1734,
Monodelphis domestica	ENSMODG00000007562	4 retrocopies	retro_mdom_1207, retro_mdom_1211, retro_mdom_1212, retro_mdom_1602,
Sarcophilus harrisii	ENSSHAG00000017878	2 retrocopies	retro_shar_19, retro_shar_47,
Taeniopygia guttata	ENSTGUG00000008426	1 retrocopy	retro_tgut_1,
Tarsius syrichta	ENSTSYG00000009667	2 retrocopies	retro_tsyr_175, retro_tsyr_74,