RetrogeneDB ID: retro_tgut_5

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 1:10407365..10408058(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000007076
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000003998
• Aliases: None
• Description: None

Sequence

>retro_tgut_5
ATGGCTCGCAACGCAGAGAAGGCCATGACGGCCTTGGCAAGATTTTGGCAAGCCCAGCTTGAGGAAGGAAAAGTCAAGGA
GCGAAGGCCTTTCCTTGCATCAGAGTGTAATGAGCTGCCCAAAGCTGAGAAATGGAGGAGACAGATCATTGGGGAGATTT
CTAAGAAAGTGGCACAGATCCAAAATGCTGGATTGGGTGAATTCAGAATTCGGGACCTGAATGATGAAATCAACAAACTT
CTGAGGGAGAAAGGACACTGGGAATACAGAATAAAGGAGCTGGGAGGTCCTGATTATGCTGGGATTGGCCCAAAAATGTT
AGATCACGAAGGGAAAGAAGTTCCAGGAAACAGAGGCTACAAATACTTTGGAGCTGCAAAGGACTTGCCAGGAGTTAGAG
AGCTTTTTGAAAAGGAGCCCCTGCCACCCCCACGGAAGACTTGGGCTGAGCTTATGAAGGACATTGACGCTGAGTACTAT
AGCTACAGGGATGAAGATGATGGGATTCTGGAGCCCCTGGAGCAGGAACATGAGAAGAAAGTTATAGCAGAAGCAGTGGC
AAAATGGAAGATGGAGAGAGAAGCACGACTTGCAAGAGGTGAGGAGGAGGAGGAGGAAGAAAACATATATGCTGTCCATG
AGGAAGAGTCTGGTGAGGAAGGTGTCAAGGAGAGAGAAGGTGAAGATGGCCAA

Alignment

ORF - retro_tgut_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.05 %
• Parental protein coverage: 76.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLGEFKIRDLNDEINKLLREKGHWEYKIKELGGPNYARIGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVR
          GLGEF.IRDLNDEINKLLREKGHWEY.IKELGGP.YA.IGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVR
Retrocopy GLGEFRIRDLNDEINKLLREKGHWEYRIKELGGPDYAGIGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVR

Parental  ELFEKEPLPPPRKTRAELMKDIDAEYYGYRDEDDGILEPLEQEHEKKVIAEAVEKWKMEREARLARG-EE
          ELFEKEPLPPPRKT.AELMKDIDAEYY.YRDEDDGILEPLEQEHEKKVIAEAV.KWKMEREARLARG.EE
Retrocopy ELFEKEPLPPPRKTWAELMKDIDAEYYSYRDEDDGILEPLEQEHEKKVIAEAVAKWKMEREARLARGEEE

Parental  EEEENIYAVHEEESDEEGGKEREGEDGQ
          EEEENIYAVHEEES.EEG.KEREGEDGQ
Retrocopy EEEENIYAVHEEESGEEGVKEREGEDGQ

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_5 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_5 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_5 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006886	1 retrocopy	retro_dord_331,
Loxodonta africana	ENSLAFG00000004015	2 retrocopies	retro_lafr_1070, retro_lafr_1170,
Myotis lucifugus	ENSMLUG00000011804	1 retrocopy	retro_mluc_1401,
Oryctolagus cuniculus	ENSOCUG00000003923	1 retrocopy	retro_ocun_1485,
Taeniopygia guttata	ENSTGUG00000003998	1 retrocopy	retro_tgut_5 ,