RetrogeneDB ID: retro_tgut_35

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: Un:129036498..129037359(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000015675
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000015754
• Aliases: None
• Description: None

Sequence

>retro_tgut_35
AAACGCAGATCACGGGGATCTGAGGGGGAAAGACCCACCCTGGGCCGGGGCGGCGGCCGGAGATGGAGCCAGAGCTCGGA
GCTGGGGGTCCCTGAGCAGCTCCATGATGGGGAGAAGCCCCACAAGTGCTCAGAGTGTGGGAAGAGCTTCAGCCACAGCT
CCAGCCTGATCGTGCACCAGAGGACCCACACTGGGGAGAAACCCTACGAGTGTGGGGAGTGTGGGAAGGGCTTCAGCCGG
AGCTCCAGCCTGATCAGGCACCAGAGAATCCACACTGGGGAACGGCCCTATGAGTGTTCCAAGTGTGGGAAGAGGTTTCG
GACCAGCTCCGATCTCCTCAGACATGAGCAGAGTCACACAGAGGAGAGGCCCTTCCACTGCCCTGACTGCGGGAAGGGAT
TCAAGGAAAACTCCAACCTCACCAGGCACCAGCGCATCCACACCGGGGAGAGGCCCTACGAGTGTGGGAAGTGTGGGAAA
GGTTTCAAAGACATGTCTCACCTGATTGAGCACCAGGTGATCCACACTGGGGAACGGCCCTATGAGTGTTTGGAATGTGG
GAAGAGCTTTGGGCGGAGCTCTACCCTGAGAACCCACCAGCGCATCCACACAGGGGAGAGGCCCTACGAGTGTCCCCAGT
GTGGGAAGAGGTTTCAGACCAGCTCCGATCTCCTCAGACATGAGCAGAGTCACACAGAGGAGAGGCCCTTCCACTGCCCC
GACTGCGGGAAGGGCTTCAAGCACAACTCCAAACTCACCATGCACCGGCGCATCCACACCGGGGAGAGGCCCTACGAGTG
TGGGAAGTGTGGGAAGAGCTTCTCCAGGAGCTCAAACTTGACCCAGCACCAGCGGAGGCAC

Alignment

ORF - retro_tgut_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.87 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKHQRIHTGERPYECPQCGKRFHTSSNLLLHERIHTEERPFRCPDCGKGFNQNSSLTRHRRIHTGERPYE
          ....R...GERP......G.R...SS.L...E..H..E.P..C..CGK.F...SSL..H.R.HTGE.PYE
Retrocopy KRRSRGSEGERPTLGRGGGRRWSQSSELGVPEQLHDGEKPHKCSECGKSFSHSSSLIVHQRTHTGEKPYE

Parental  CLECGKGFSWSSNLIRHQRIHTGERPYECGECGKRFRTSSDLLLHERSHTEERPFRCPDCGKGFNRNSHL
          C.ECGKGFS.SS.LIRHQRIHTGERPYEC..CGKRFRTSSDLL.HE.SHTEERPF.CPDCGKGF..NS.L
Retrocopy CGECGKGFSRSSSLIRHQRIHTGERPYECSKCGKRFRTSSDLLRHEQSHTEERPFHCPDCGKGFKENSNL

Parental  TEHRRIHTGERPYECGKCGKGFKDRSLLIKHQVIHTGERPYECLECGKSFGWSSHLRIHQRIHTGERPYE
          T.H.RIHTGERPYECGKCGKGFKD.S.LI.HQVIHTGERPYECLECGKSFG.SS.LR.HQRIHTGERPYE
Retrocopy TRHQRIHTGERPYECGKCGKGFKDMSHLIEHQVIHTGERPYECLECGKSFGRSSTLRTHQRIHTGERPYE

Parental  CPQCGKRFRTSSHLLLHERSHTEERPFRCPDCGKGFNRNSSLTVHRRIHTGERPYECWKCGKSFSQSSNL
          CPQCGKRF.TSS.LL.HE.SHTEERPF.CPDCGKGF..NS.LT.HRRIHTGERPY.......SFS.SSNL
Retrocopy CPQCGKRFQTSSDLLRHEQSHTEERPFHCPDCGKGFKHNSKLTMHRRIHTGERPYXXXXXXXSFSRSSNL

Parental  TQHQRRH
          TQHQRRH
Retrocopy TQHQRRH

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_35 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_35 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Taeniopygia guttata	ENSTGUG00000013808	2 retrocopies	retro_tgut_29, retro_tgut_33,
Taeniopygia guttata	ENSTGUG00000015384	1 retrocopy	retro_tgut_40,
Taeniopygia guttata	ENSTGUG00000015754	1 retrocopy	retro_tgut_35 ,