RetrogeneDB ID: retro_gacu_24

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: scaffold_111:317896..318349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: suv420h2
• Ensembl ID: ENSGACG00000013526
• Aliases: None
• Description: suppressor of variegation 4-20 homolog 2 (Drosophila) [Source:ZFIN;Acc:ZDB-GENE-080523-2]

Sequence

>retro_gacu_24
AGTAATCGTCAGCAACTGCTAAGGAAACGGGTCCATCACTACCTCAGTGCCTTGCTGTTGGACAGTGGTCTGAGCATAGA
GTCCATAGTGAGATACTCCTGTGAGAATACTGGAGCGAAGGTAACCGCGACAAGGCACTGGCTTCCAGGACAGCGCATCA
AGGTCCTGCTGGGCTGCATAGCAGAGTTCACTCCTGCCGACAGTGCTGTGCTGAAGGCTGGAGTGAATGACTTCAGCGTG
ATGTATTCCATGAGAAGAAAACGCAATCAGCTCGGACCTGCACGTCTCGTGAACCACGACTGCCATCCCAATGTCAAATA
AGTTGCCTGCAAGTCCGTGGCTTCCGTAGTTGTGGTTAGATCCATCTCACCTGGCGAGGAGATCACCTGCTTTTATGGTC
CAAACTTTTTGGAAGACAAAAATGAGTTGTGTGAATGCTGCACCTGTGACAGG

Alignment

ORF - retro_gacu_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHRQELLRQHVYRYLSAFLLDNGIKIESCDRYSSETNGAKITSTRQWFAGERVEVLLGCIAELSPADGTV
          S.RQ.LLR..V..YLSA.LLD.G..IES..RYS.E..GAK.T.TR.W..G.R..VLLGCIAE..PAD..V
Retrocopy SNRQQLLRKRVHHYLSALLLDSGLSIESIVRYSCENTGAKVTATRHWLPGQRIKVLLGCIAEFTPADSAV

Parental  LRAGVNDFSVMYSTRKRCTQLWLGPAAFINHDKDCKPNCKFVPGEKNIACVEAIRPISPGEEITCYYGAS
          L.AGVNDFSVMYS.R....Q..LGPA...NH..DC.PN.K.V...K..A.V...R.ISPGEEITC.YG..
Retrocopy LKAGVNDFSVMYSMRRKRNQ--LGPARLVNH--DCHPNVK*V-ACKSVASVVVVRSISPGEEITCFYGPN

Parental  FFGEGNEMCECCTCER
          F....NE.CECCTC.R
Retrocopy FLEDKNELCECCTCDR

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_24 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000013526	1 retrocopy	retro_gacu_24 ,