RetrogeneDB ID: retro_drer_23

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 13:14578693..14579272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: gyg1a
• Ensembl ID: ENSDARG00000011934
• Aliases: gyg1a, fc13d04, fi23f07, gyg, gyg1, wu:fc13d04, wu:fi23f07, zgc:55385, zgc:85619
• Description: glycogenin 1a [Source:ZFIN;Acc:ZDB-GENE-040426-2910]

Sequence

>retro_drer_23
TCTGGTATGTTTGTCTTCCGCCCCTCCAATGAGACCTATGGGAAACTCATCACCGCCTGTTCAGTGGGTGGCAGCTTTGA
TGGTGGGGATCAGGGTGTCCTCAACAGCTTCTTCAGTGATTGGGCAACAGCAGACATTTCAAAACACCTTCCGTTCATCT
ACAACCTCAGCAGCATCGCCATCTACACTTATCTCCCAGCATTCAAGCAATACGGCCATGATGCCAAGGTAGTTCATTTC
CTTGGCAAAGTCAAACCATGGGATTACAGTTTTGACACTGCAAGCAAAACGGTCAAGGGACAGTCCCACGATGCTGATAT
GCACCCCAACTACCTGCTGCAGTGGTGGGAGCTGTTCAGTTCTTCAGTGTTGGCTCTCATGAAGGAGGAGTACGGGGACC
AACCCTTCTATTCTGGTTGCACAGAGGGTGATATCCATGTTGACATGGGTCAGATGCACTTATCCCATCCCCCTTCACCT
CCGATGTCATCTAAGGAGCGGAAGAAGAAGTGGGAACAGGGTCAAGCGGACTACATGGGAATGGACTCTTTTGACAACAT
AGAAAAAAACCTAGATAAC

Alignment

ORF - retro_drer_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.37 %
• Parental protein coverage: 58.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGVFVFRPSNETYGKLITACSEGGSFDGGDQGVLNSFFSDWATADISKHLPFIYNLSSIAIYTYLPAFKQ
          SG.FVFRPSNETYGKLITACS.GGSFDGGDQGVLNSFFSDWATADISKHLPFIYNLSSIAIYTYLPAFKQ
Retrocopy SGMFVFRPSNETYGKLITACSVGGSFDGGDQGVLNSFFSDWATADISKHLPFIYNLSSIAIYTYLPAFKQ

Parental  YGHDAKVVHFLGKVKPWDYSFDTASKTVKGQSHDADMHPNYLLQWWELFSSSVLALMKEEYGDQPFYSGC
          YGHDAKVVHFLGKVKPWDYSFDTASKTVKGQSHDADMHPNYLLQWWELFSSSVLALMKEEYGDQPFYSGC
Retrocopy YGHDAKVVHFLGKVKPWDYSFDTASKTVKGQSHDADMHPNYLLQWWELFSSSVLALMKEEYGDQPFYSGC

Parental  TEGDIHVDVGQMHLSHPPSPPMSSQERKQKWEQGQADYMGMDSFDNIEKKLDS
          TEGDIHVD.GQMHLSHPPSPPMSS.ERK.KWEQGQADYMGMDSFDNIEK.LD.
Retrocopy TEGDIHVDMGQMHLSHPPSPPMSSKERKKKWEQGQADYMGMDSFDNIEKNLDN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_drer_23 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_23 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001467	2 retrocopies	retro_cjac_1049, retro_cjac_2915,
Danio rerio	ENSDARG00000011934	1 retrocopy	retro_drer_23 ,
Homo sapiens	ENSG00000163754	2 retrocopies	retro_hsap_1222, retro_hsap_159,
Myotis lucifugus	ENSMLUG00000006382	1 retrocopy	retro_mluc_2351,
Macaca mulatta	ENSMMUG00000005521	2 retrocopies	retro_mmul_1297, retro_mmul_376,
Nomascus leucogenys	ENSNLEG00000002557	2 retrocopies	retro_nleu_1556, retro_nleu_693,
Oryctolagus cuniculus	ENSOCUG00000003516	1 retrocopy	retro_ocun_1766,
Pongo abelii	ENSPPYG00000025899	2 retrocopies	retro_pabe_1015, retro_pabe_1080,
Pan troglodytes	ENSPTRG00000015509	1 retrocopy	retro_ptro_836,