RetrogeneDB ID: retro_tgut_27

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 7:24509039..24509618(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000010715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000000876
• Aliases: None
• Description: None

Sequence

>retro_tgut_27
CTGGGCTGTCATTCTTTCACCAGGTCCTTCCTGGAGTATTTTGCTGCTGATGTCAGCTACCCAGTGAGGAAGGAGGGATA
CCAGAGTGTGGTGCAGATGGCATTCCCAAACACAAAGGAGGAAGGTGATGGACAGTCTTCCTCAGACACTTCCCTCAGAA
ACCCACCAGGAGGCTTCTTCCTGACAGGATCAGAGCTGCCAGGGATAGGGAGAACAGGAAGCTGGTGGAGTTCATAGTGA
AGACCAAAGGGGCTGAAGAGCATCTCCTGGGGATCTTGAAAAGTGGGAAACAATCCCACTGGCTGAAGAAATTCCTGAGT
TCCAGCTGGTACATGACCTGTGTGGAGGCTTATTTGGAGGATGAAGAACAGCTGGACCTGGTGCTTGGGTTCCTGAAGGA
GGTGTACAAGGAGGTGGACACCAAGAACGTACACCAGATCCTGGGGGATGGCATCAGATTCATCTCAAATGCGCTTTTTA
CCTAAAGCTATCATCTGTGCCGTTGCTGCTGTGGATGACATTGATTATGAGAAGGCAAAAGAGCAGTATATTAAAGGACT
ACCTGTGAGCAAAAGAAAG

Alignment

ORF - retro_tgut_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.64 %
• Parental protein coverage: 64.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGCHSFTGSFLEYFAADISYPVRKEGYQSVVQMAFPNAGEEGAGQSSSDTS-PQKPPRRLLPDRTRAARD
          LGCHSFT.SFLEYFAAD.SYPVRKEGYQSVVQMAFPN..EEG.GQSSSDTS.PQKP.RRLLPDR.RAARD
Retrocopy LGCHSFTRSFLEYFAADVSYPVRKEGYQSVVQMAFPNTKEEGDGQSSSDTS<PQKPTRRLLPDRIRAARD

Parental  RENKKLVEFIVKTKGAEEHLLGILKSGKQSRWLKKFLNSSQYMTCVETYLEDEEQLDLVVGYLKEVYREM
          REN.KLVEFIVKTKGAEEHLLGILKSGKQS.WLKKFL.SS.YMTCVE.YLEDEEQLDLV.G.LKEVY.E.
Retrocopy RENRKLVEFIVKTKGAEEHLLGILKSGKQSHWLKKFLSSSWYMTCVEAYLEDEEQLDLVLGFLKEVYKEV

Parental  DTKNLHQILGDGIRFILDVL-LPEAIICAIAAVDDIDYEKAEEKYIKGPPVSKRE
          DTKN.HQILGDGIRFI...L.LP.AIICA.AAVDDIDYEKA.E.YIKG.PVSKR.
Retrocopy DTKNVHQILGDGIRFISNAL>LPKAIICAVAAVDDIDYEKAKEQYIKGLPVSKRK

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_27 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_27 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003299	1 retrocopy	retro_amel_86,
Taeniopygia guttata	ENSTGUG00000000876	1 retrocopy	retro_tgut_27 ,