RetrogeneDB ID: retro_drer_12

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 10:19598884..19600180(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000078394
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CABZ01059627.1
• Ensembl ID: ENSDARG00000079681
• Aliases: None
• Description: None

Sequence

>retro_drer_12
AGTTCAGCTTCACAAGGTACCACCTATGGTGTAATTACCCAGGCTCAAGGTGCAAGTCAGTCTGCTCCAGGATCTTCATC
CCCATATACAACCATATCATTGCCCAAATATGTTACTAGTCAGTTGATAACTGGACCAAGTTCAAAGCAATTTACCTCCG
TCTATGGCACCCAGACAGGATCCTCTGCCCCTTTTACTTTGAAAGAAAGTACCACATATGGTGAACAAATCCAGACTCAA
GATGCCACAAGTCAATTAGTTTTGGGATCTTCAAACCCTTACGCATCTGTATCATCACCTCAAGTTGTTACAAGTCAGTT
GACGCCTGTGCCAGGTTCGAAGCAGGTTACATCTGTCTATGGCACTCAGACTGGTTCTTTTGCTCCCTTCACTCTGCAAA
AACTATTCCAGGGTAAAGGTTCAACAAGCCCGGTTTTTTCAGTACCTTCAACCTCATACGCCTCTGTATCATTGCCCCAA
GGTGTTACTAGTCAGTCGACCACAGTGCCAAGTTCAAAGCAGATAACCTCTGTCTACCCCACCCAGACAGGATCCTCTGC
CCCTTTCACTTTGCAAGAACTACTCCAGGGTCCAGATTCAACAAGTCAGGTTGTTTATGGATCTTCAACCCCATATGTAT
CTTTATCATTACCCCAAAGTGTTACTAGTCAGTCAACGACAGTGCCAAGTTCAAAGCAGATAACCTCTGTCTATACCACC
CAGGCAGGATCCTCTGTCCCTTTCACTTTGCAAGAACTACTTCAGGGTCAAGATTCAACAAGCCAGGTTGTTTATGAATC
TTCAACCCCATATGTATATTTATCATCGCCCCAAGTTGTTACTAGTCAGTTGACACCTGTGTCAGGTTCAAAGCAGGTTA
CACCCGTGTATACAACCCAGACAGGATCCTCTGTCCCTTTCACTTTGCAAGGACTACTCCAGGGTCAAGATTCAACAAGT
CAGGTTGTTTATGGTTCTTCATTCCCATACTTATTTGTATCGACGCCCCAAGTTGTTACTAGCCAGTTGACACTTGTGCC
AAGTTCAAAGCAGGTTACCACTGTCTATGGCACTCAGACTGATTCTTCGGCTCCCTTCACTCTGCAAAAACTACTTCAGG
GTAAAGGTTCAACAAGCCAGGTTGTTTCAGAACCTTCAACCCCGTATGTATCTGTATCATTGCCACAAGTTGTAACTAGT
CAGACGTATAAAGTGCCAAGTTCGAAGCAGGTAACCTCTGTCTACACCACCCAGACAGGATCCTCTGCCCCTTTCACTTT
GCAAGAACTACTCCAG

Alignment

ORF - retro_drer_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSASQGTTYGVITQAQGASQSAPGSSSPYTTISLPKYVTSQLITGPSSKQFTSVYGTQTGSSAPFTLKES
          SSASQGTTYGVITQAQGASQSAPGSSSPYTTISLPKYVTSQLITGPSSKQFTSVYGTQTGSSAPFTLKES
Retrocopy SSASQGTTYGVITQAQGASQSAPGSSSPYTTISLPKYVTSQLITGPSSKQFTSVYGTQTGSSAPFTLKES

Parental  TTYGGQIQTQDATSQLVLGSSTPYISVSSPQVVTSQLTPVPGSKPVTSVYGTRTGSSAPFTLQRLLQGKG
          TTYG.QIQTQDATSQLVLGSS.PY.SVSSPQVVTSQLTPVPGSK.VTSVYGT.TGS.APFTLQ.L.QGKG
Retrocopy TTYGEQIQTQDATSQLVLGSSNPYASVSSPQVVTSQLTPVPGSKQVTSVYGTQTGSFAPFTLQKLFQGKG

Parental  STSQVVSVPSTPYIAVSLPQGVTSLSTPVSSSKQVTSVYTTQTGPSAPFTLQELLQGQDATSQFVSGSSS
          STS.V.SVPST.Y..VSLPQGVTS.ST.V.SSKQ.TSVY.TQTG.SAPFTLQELLQG.D.TSQ.V.GSS.
Retrocopy STSPVFSVPSTSYASVSLPQGVTSQSTTVPSSKQITSVYPTQTGSSAPFTLQELLQGPDSTSQVVYGSST

Parental  PYVAVSMPQVVTSQS-AVPCSKQVTSVYGTQTGSSAPFTLQRLLQGKDATSKLVLASSTPYVSVSSPQVV
          PYV..S.PQ.VTSQS..VP.SKQ.TSVY.TQ.GSS.PFTLQ.LLQG.D.TS..V..SSTPYV..SSPQVV
Retrocopy PYVSLSLPQSVTSQSTTVPSSKQITSVYTTQAGSSVPFTLQELLQGQDSTSQVVYESSTPYVYLSSPQVV

Parental  TSQLTPVPGSKPVTSVYTTQTGSSVPFTLQGVLQGQDSTSQVVYGSSTPYVSVSLPQDVTSQLTPVPSSK
          TSQLTPV.GSK.VT.VYTTQTGSSVPFTLQG.LQGQDSTSQVVYGSS.PY..VS.PQ.VTSQLT.VPSSK
Retrocopy TSQLTPVSGSKQVTPVYTTQTGSSVPFTLQGLLQGQDSTSQVVYGSSFPYLFVSTPQVVTSQLTLVPSSK

Parental  QVTSVYTTQTGSSAPFTLQGVLQGQDATSQFVSRSLSPYVAFSLPQVVTSQS-AVPSSKQITSVYGTRTG
          QVT.VY.TQT.SSAPFTLQ..LQG...TSQ.VS....PYV..SLPQVVTSQ...VPSSKQ.TSVY.T.TG
Retrocopy QVTTVYGTQTDSSAPFTLQKLLQGKGSTSQVVSEPSTPYVSVSLPQVVTSQTYKVPSSKQVTSVYTTQTG

Parental  SSAPYTLQ
          SSAP.TLQ
Retrocopy SSAPFTLQ

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

7 EST(s) were mapped to retro_drer_12 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM071978	19599275	19599707	98.4	424	7	417
BQ263746	19598907	19599541	98.2	622	12	610
BQ263821	19598910	19599421	98.5	503	8	495
DY552011	19598908	19599606	97.9	690	8	679
DY574386	19598908	19599605	97.8	688	9	676
EB880570	19599345	19599749	95.8	391	12	377
EV558591	19598932	19599376	98.7	438	6	432

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_12 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
Danio rerio	ENSDARG00000079681	1 retrocopy	retro_drer_12 ,