RetrogeneDB ID: retro_tgut_36

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: Un:133933549..133934077(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000016195
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000016647
• Aliases: None
• Description: None

Sequence

>retro_tgut_36
GAGCAGCCTCCATGACAGGGGGAGGCCCTACCAGTGGCTCGGAGTGTGGGAAGAGCTTCAGGAAGAATTTCAACTGATCT
GCACAGAGGATCACACTGGGGAACGGCTTACGAGTGTGGGGAGTGTGGGAACAGCTTCAGCCACAGGTCCGGCCTGGATT
TCCCCCCAGAGGTTCCACACGGGGGAGAGGCCCTACGAGTGTCCTGAGTGTGGGAAGAGGTTTCACACCAGCTCCCATCT
CCTTGTCCATCAGCGGATTCACAGACAGGAGAGGCCCTTCCGCTGCCCCGACTGCGGGATGGGCTTCAAGCACAACTCCA
CCCTCGTCACCCACTGGCGCATCCACACCAGGGAGAGGCCCTACGAGTGTCCCCGGTGTGGGAAGAGCTTCTCAGACCGC
TCATTCTTTACCCGGCACCAGCGGAGGCACCGGTAAGGGAAGCCCTGTGAGAACCCCGCCTGCAGGAAGAGCTTTGTGCG
CTGCTCCAGCTCCATCCCCATCAGAGGACCCACCCTGGTCAGTGTCCC

Alignment

ORF - retro_tgut_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.5 %
• Parental protein coverage: 63.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EQP-HDRERPYEC-SECGKSFRKNFN-LICHQRIHTGER-PYECEECGNSFSHRSDL-IVHQRFHTGERP
          EQP.HDR.RPY...SECGKSFRKNFN.LIC....HTGER..YEC.ECGNSFSHRS.L.I..QRFHTGERP
Retrocopy EQP>HDRGRPYQW>SECGKSFRKNFN<LICTED-HTGER<AYECGECGNSFSHRSGL>ISPQRFHTGERP

Parental  YECPECGKRFHTSSHLLVHQRIHRQERPFRCPDCGMGFKHNSTLVTHQRIHTGERPYECPRCGKSFSDRS
          YECPECGKRFHTSSHLLVHQRIHRQERPFRCPDCGMGFKHNSTLVTH.RIHT.ERPYECPRCGKSFSDRS
Retrocopy YECPECGKRFHTSSHLLVHQRIHRQERPFRCPDCGMGFKHNSTLVTHWRIHTRERPYECPRCGKSFSDRS

Parental  FFTRHQRRHREERPTLGQEGGQSFRQSS-KLMVHEKLHDGEKP
          FFTRHQRRHR...P........SF...S..L..H...H.G..P
Retrocopy FFTRHQRRHR*GKPCENPACRKSFVRCS<QLHPHQRTHPGQCP

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_36 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_36 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
Taeniopygia guttata	ENSTGUG00000016647	1 retrocopy	retro_tgut_36 ,
Taeniopygia guttata	ENSTGUG00000016956	1 retrocopy	retro_tgut_28,