RetrogeneDB ID: retro_drer_3

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 5:67435937..67436528(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000032976
• Aliases: cmlc1, zgc:103441
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: zgc:114164
• Ensembl ID: ENSDARG00000011519
• Aliases: myl4, im:7136900, zgc:114164
• Description: zgc:114164 [Source:ZFIN;Acc:ZDB-GENE-050626-112]

Sequence

>retro_drer_3
ATGGCACCAAAAAAAGTGGAACCCAAGAAACCAGAGCCGAAAAAACCTGAGGCCAAAAAAGAAGAAGCCCCTGCTCCTGC
ACCAGTTCCAGAGACACCCAAAGAGCCCGAAGTGGACCTGAAAAGCGTCCCGCTGGATTTTAGCCCAGACCAGATTGAAG
AGTTCAGGGATGCCTTTACTCTCTTTGATGAAACGCCAACAGGAGAGATGAAGATAAGGTATGCCCAGTGTGGAGATGTG
ATGAGGGCTCTGGGTCACAACCCTACCAATGCTGATGTATTGACGGTATTAGGGAAGCCCAAAGCTGAAGAAATGAACAC
CAAATACCTGGACTTTGAGACGTTCCTGCCAATGCTGCAGCATATCTCAAGAGCCAAGGACCAGGGGACGTTTGAGGACT
TTGTTGAGGGTCTGAGAGTCTTTGACAAAGAGGGAAACGGAACAGTGATGGGTGCTGAGCTCCGTCACGTCTTGGCAACG
CTTGGGGAGAAAATGACAGAGGATGAGGTGGACCGTCTGATGGCCGGACAAGAAGACGCCAACGGCTGCATTAACTACAC
GTCCTTCATCAAGCACATCCTCTCCGGGTGA

Alignment

ORF - retro_drer_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 98.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKKAEPKKEAAK----PAPPPEPEKPKEPQFDLKSIKVEFTADQIEEFKETFMLFDRTPASEMKITYAQC
          PKK.EPKK..AK....PAP.P.PE.PKEP..DLKS....F..DQIEEF...F.LFD.TP..EMKI.YAQC
Retrocopy PKKPEPKKPEAKKEEAPAPAPVPETPKEPEVDLKSVPLDFSPDQIEEFRDAFTLFDETPTGEMKIRYAQC

Parental  GDVMRALGLNPTNAEVLKVLGKPRPEEMNTKMIDFETFLPMFQHVSRSKDQGTFEDFVEGLRVFDKEGNG
          GDVMRALG.NPTNA.VL.VLGKP..EEMNTK..DFETFLPM.QH.SR.KDQGTFEDFVEGLRVFDKEGNG
Retrocopy GDVMRALGHNPTNADVLTVLGKPKAEEMNTKYLDFETFLPMLQHISRAKDQGTFEDFVEGLRVFDKEGNG

Parental  TVMGAELRHVLATLGEKMTESEVEQLMAGQEDGNGCVNYEAFVKHIMAG
          TVMGAELRHVLATLGEKMTE.EV..LMAGQED.NGC.NY..F.KHI..G
Retrocopy TVMGAELRHVLATLGEKMTEDEVDRLMAGQEDANGCINYTSFIKHILSG

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_3 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_3 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013199	1 retrocopy	retro_chof_2215,
Danio rerio	ENSDARG00000011519	1 retrocopy	retro_drer_3 ,
Pteropus vampyrus	ENSPVAG00000004194	1 retrocopy	retro_pvam_841,
Tetraodon nigroviridis	ENSTNIG00000008476	1 retrocopy	retro_tnig_18,