RetrogeneDB ID: retro_olat_52

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold2790:2339..2717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000019703
• Aliases: None
• Description: None

Sequence

>retro_olat_52
CTCCTCCAGTGTTGGATGACTAAAGAGGAAGATCTCTGCATCCATCAGAGGAGCTTCAGAGTAGAACGGGAAGAACCACA
ACTTCCACAGATTAAAAAGGAACCAGGGGAACTCTACATCAGTCAGGATGAAGATCAGCTTGATCTGAAGCAGGAGACTG
ATACCTTGATGGAGATTCCTACTTATGAGGAAGACGAGAACAGTGAAGCAGATCTAAACAATCAGCAGAGCTTTAATGTA
ACTGATAGTCAGGATGAAGAAGGAAACCAACATGAAGAATCAACATCAACTACAGATGAAGAGACAGGCCCACAGAACAG
AGATCAGAGGAAGAGGAGGGACAGAAGTCAAGTCCAAAGTGTGGACAGCTCTCACGTG

Alignment

ORF - retro_olat_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.92 %
• Parental protein coverage: 68.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPQHWMTEEEDLCNQQRNFRVEQEEPEPPQIKEEPEELCISQDEDHLHLKQETDTLMEIPTYEEDENSEA
          L.Q.WMT.EEDLC..QR.FRVE.EEP..PQIK.EP.EL.ISQDED.L.LKQETDTLMEIPTYEEDENSEA
Retrocopy LLQCWMTKEEDLCIHQRSFRVEREEPQLPQIKKEPGELYISQDEDQLDLKQETDTLMEIPTYEEDENSEA

Parental  DLNNQQSFNVTDSQDEEGNQHEESTSTTDEETDPQNRDKRKRRDRRHVQSVDSSHM
          DLNNQQSFNVTDSQDEEGNQHEESTSTTDEET.PQNRD.RKRRDR..VQSVDSSH.
Retrocopy DLNNQQSFNVTDSQDEEGNQHEESTSTTDEETGPQNRDQRKRRDRSQVQSVDSSHV

Legend:

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

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_52 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_52 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_52 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000018644	1 retrocopy	retro_olat_44,
Oryzias latipes	ENSORLG00000019703	11 retrocopies	retro_olat_39, retro_olat_45, retro_olat_46, retro_olat_47, retro_olat_49, retro_olat_50, retro_olat_52 , retro_olat_54, retro_olat_58, retro_olat_60, retro_olat_63,
Oryzias latipes	ENSORLG00000020272	1 retrocopy	retro_olat_34,