RetrogeneDB ID: retro_tgut_29

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: Un:35612037..35612634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000013808
• Aliases: None
• Description: None

Sequence

>retro_tgut_29
GAAAGACCCAGACTGTGCCAGGGAGATGGGCAGAGTTTCAGCCAGAGCTCAGAGCTGGTGGTCCGTCAGCAGCTTCAAGA
CAGGGAGAGGCCCTATGAGTGCTTGGAGTGTGGGAAGAGCTTCAAGAGGATCTCCAGCCTGGTTCACCACCAGAGGATCC
ACACTGGGGAACGGCCTTATGAGTGTGGGGAGTGTGGGAAGAGCTTCAGATTCAAGTCCAACCTGATTGCCCACCTGAGG
TTCCACACCAGGGAGAGGCCTTACGAGTGTCCCAAGTGTCAGAAGAGGTTTCACACCAACTCCTGTCTCCTCCACCACTA
TCGGGTCCACACAGAGGAGAGGCCCTTCTGCTGCCCCGACTGCGGGAAGAGCTTCAACCGCAACTCCCACCTCACCAGGC
ACCGGCGCATCCACACCGGGGAGAGGCCCTACGAGTGTGGGGAGTGTGGGAAGAGCTTCTCACAGAGCTCTCACTTGACC
CAGCACCAACGGAGGCACCGGTGAGTGAAGCCTTGCAAATGCCCCAGCTGCAGGAAGAGCTTTTTGCCCTGTTCCAACTC
CATCACCCAGGGGAGCACCCATGTTGGGAGGAGCCCT

Alignment

ORF - retro_tgut_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.14 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERPRLCQGDGQSFSQSSELVVRQQLQDRERPYECLECGKSFKRISSLVHHQRIHTGERPYECGECGKSFR
          ERPRLCQGDGQSFSQSSELVVRQQLQDRERPYECLECGKSFKRISSLVHHQRIHTGERPYECGECGKSFR
Retrocopy ERPRLCQGDGQSFSQSSELVVRQQLQDRERPYECLECGKSFKRISSLVHHQRIHTGERPYECGECGKSFR

Parental  FKSNLIAHLRFHTRERPYECPKCQKRFHTNSCLLHHYRVHTEERPFCCPDCGKGFKHNSHLTRHRRIHTG
          FKSNLIAHLRFHTRERPYECPKCQKRFHTNSCLLHHYRVHTEERPFCCPDCGK.F..NSHLTRHRRIHTG
Retrocopy FKSNLIAHLRFHTRERPYECPKCQKRFHTNSCLLHHYRVHTEERPFCCPDCGKSFNRNSHLTRHRRIHTG

Parental  ERPYECGECGKSFTQSSHLTQHQRRHRGAFPRLPGCCSCRGQSFSQSSELVVPEKLHDGEKP
          ERPYECGECGKSF.QSSHLTQHQRRHR...P....C.SCR..SF...S........H.G..P
Retrocopy ERPYECGECGKSFSQSSHLTQHQRRHR*VKP--CKCPSCR-KSFLPCSNSITQGSTHVGRSP

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_29 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_29 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,