RetrogeneDB ID: retro_tgut_1

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 4A:5689360..5690131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000002696
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000008426
• Aliases: None
• Description: None

Sequence

>retro_tgut_1
ATGGTGGGGGTGAAGAGCAGCGCTCTCTCCTTGCTGGAGGTTTACACCGGGGACTCGGAGCCGGAGTGGGACAGCGAGGC
CGGCACGGCAGGGAGCGATGGGGCAGCGCCCACGGGGGAGAAAGGAGGCCTGGTGTCAGCTGGGTATGGAGAAGGTGACT
TCACCCGCCTGGATGGGGATGAGGAAGGGTACGAAGAGGAGGCGGAGGACGGGAACAGCAGGCAGTCAGAAGATGACAAC
TCACAGACTGAAAAACCTGAGGCTGGTGACCTAAAGAAATTCCGAGAAGTGGAGGAAAGAGATCCTCAGGAGCTGGTTCC
TTCTTTTTCAGAGACAGTGTGGAACATGTCTCCAGATGAGATCAAAATCCCACCTGAGCCTCTTGGCAGCTGTTCTAACC
AATTGCAAGATAAAATTAAAAAGCTGTATGAGTGGAAAATGAAAGAGGGCATAGATATGAACTACATCATCCAGAACAAA
AAGGAATTTTGCAATCCCAGCATCTATGAAAAGCTGATCCAGTTTTGTTCCATTGATGAAATTGGTACAAATTACCCAAA
GGACATGTTTGATCCTCACAGCTGGTCAGAGGATTCGTATTATGAAGCACTAGCTAAAGCCCAGAAGACCGAGATGGACA
AATTGAAGAAGGCCAAGGAAGAACGTACAAAGATTGAATTTGTGACTGGCATTAAAAAAGGTACAAGAAGAAGCGCTGCT
TCCACAACCACAACATCCAGCACCACTGTGGGGGATGCCCAGAAGAAGAGG

Alignment

ORF - retro_tgut_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 82.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAKRSVLSSLAVYAEDSDPESDSEAGTAGSDGGAPTGEKGGLVSVGYGEDDFNRLDGDEEGYEEE-DD
          M...K.S.LS.L.VY..DS.PE.DSEAGTAGSDG.APTGEKGGLVS.GYGE.DF.RLDGDEEGYEEE..D
Retrocopy MVGVKSSALSLLEVYTGDSEPEWDSEAGTAGSDGAAPTGEKGGLVSAGYGEGDFTRLDGDEEGYEEEAED

Parental  ENSRQSEDDDSETEKPEAGDLKEFSEVEKRDPQELVASFSERVRNMSPDEIKIPPEPPGRCSNQLQDKIQ
          .NSRQSEDD.S.TEKPEAGDLK.F.EVE.RDPQELV.SFSE.V.NMSPDEIKIPPEP.G.CSNQLQDKI.
Retrocopy GNSRQSEDDNSQTEKPEAGDLKKFREVEERDPQELVPSFSETVWNMSPDEIKIPPEPLGSCSNQLQDKIK

Parental  KLYERKVKEGMDMNYIIQRKKEFRNPSIYEKLIQFCSIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKI
          KLYE.K.KEG.DMNYIIQ.KKEF.NPSIYEKLIQFCSIDE.GTNYPKDMFDPH.WSEDSYYEALAKAQK.
Retrocopy KLYEWKMKEGIDMNYIIQNKKEFCNPSIYEKLIQFCSIDEIGTNYPKDMFDPHSWSEDSYYEALAKAQKT

Parental  EMDKLEKAKKERTKIEFVTGTKKGTTTSAASTTTTTSSTTVGDAQKRK
          EMDKL.KAK.ERTKIEFVTG.KKGT..SAAS.TTTTSSTTVGDAQK..
Retrocopy EMDKLKKAKEERTKIEFVTGIKKGTRRSAAS-TTTTSSTTVGDAQKKR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Taeniopygia guttata was not studied using RNA-Seq expression data.

ChIP-Seq

Taeniopygia guttata was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tgut_1 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_1 has 0 orthologous retrocopies within neognath group .

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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,