RetrogeneDB ID: retro_tgut_40

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: Un:135520082..135520670(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000015384
• Aliases: None
• Description: None

Sequence

>retro_tgut_40
GAAAGGCCCACCCTGGGTCAGGAAGGTGGGCAGAGCTTCAGCCAGAGCTTGGAGGTGGTGGTCCATGAGAAGCTTCACGA
TGGGGAGAAGCCCTACAAGTGCTTGGAGTGTGGGAAGAGCTTCAGGAACAGCAACAACCTGATCCGCCACCAGATGGTCC
ACACTGGGGAATGGGCCTGTGAGTGTGGGGAGTGTGGGAAGGGATTCAGCTGCAGCTCTGCCCTTGTCACCCACCAACGC
ATCCACACTGGGGAGAGGCCCTACGAGTGTCCGGAGTGTCAGAAGAGGTTTCACAGCAGCTCTGATCTCCTCAAACACCA
GCGGATTCACACGGATGAGAGGCCCTTCCGCTGCCCCGACTGCGGGAAGGGCTTCAAGCACAACTTCACCCTTGTCAGGC
ACCGGCGCATTCACACCGGGGAGAGGCCCTACAAGTGTCCCCATTGTGGGAAGAGCTTCACCCAGAGCTCTCACTTGACC
AGACACCAACAGGGGCACCGGTAAGGGAAACCCTGGGATTTCCCCGAGTGTGGGAAGAGCTTCGTGCTCTGCTCCAGCTC
CATCCCCCACTGGAGAACCCACATTGGG

Alignment

ORF - retro_tgut_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 64.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERPTLGQESGQSFSQSSDLVVHEKLHDGEKPYKCLECGKSFRKSNTLIRHQMIHTGEWAYECGECGKGFS
          ERPTLGQE.GQSFSQS...VVHEKLHDGEKPYKCLECGKSFR.SN.LIRHQM.HTGEWA.ECGECGKGFS
Retrocopy ERPTLGQEGGQSFSQSLEVVVHEKLHDGEKPYKCLECGKSFRNSNNLIRHQMVHTGEWACECGECGKGFS

Parental  CSSALVAHQRIHTGERPYECPECQKRFHSSSDLLKHQRIHTDERPFRCPNCGKGFKHNFTLVRHRRIHTG
          CSSALV.HQRIHTGERPYECPECQKRFHSSSDLLKHQRIHTDERPFRCP.CGKGFKHNFTLVRHRRIHTG
Retrocopy CSSALVTHQRIHTGERPYECPECQKRFHSSSDLLKHQRIHTDERPFRCPDCGKGFKHNFTLVRHRRIHTG

Parental  ERPYGCPQCGKSFTQSSHLTRHQRGHRDGSKPYKCLECGKSFRKSNTLIRHQMIHTG
          ERPY.CP.CGKSFTQSSHLTRHQ.GHR.G.KP....ECGKSF......I.H...H.G
Retrocopy ERPYKCPHCGKSFTQSSHLTRHQQGHR*G-KPWDFPECGKSFVLCSSSIPHWRTHIG

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_40 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_40 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,