RetrogeneDB ID: retro_olat_14

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold2516:2990..3638(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000019958
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSORLG00000001047
• Aliases: None
• Description: None

Sequence

>retro_olat_14
AACTCTGGTGTCACAGTGAAGCTGCGGACCCGGCTGCTGGTGTCGCTGCTGTTTGGCGGCGGGCTGCTTGGGGCGTGGGC
GTACGTGTACTGGGAGAAGCAGCAGCGGCGGTGGCAGCAGCGGACCGAGCAGCTCCGGAAGGTGGCTCTGGGCCAGGGCA
CCTTCAGCCTGGTCGACCACACGGGCCGGCGGCGGACCAAGCAGGACTTCCTGGGCAGCTGGGTGCTGCTGTATTTTGGG
TTCACGCACTGCCCAGACATCTGCCCCGACGAGCTGGACAAGCTGAGCGCTGCGGTGGCAGTTCTGGACCAGGACGCCTC
GCTGCCCCCTGTCCAGCCCCTCTTCATCACCGTGGACCCGGAGAGGGACGGCGTGCCGGCCTTGGCCCGCTACGTCAAGG
ACTTTCACCCGCGGCTGATCGGCTTGACCGGTACCCCGGAGGAGGTGAAGCACGCGGGGCGGGACTACCGGGTGTACGCC
AGCCCCGGGCCCAAAGACCAGGACGGAGACTACATCGTGGACCACAGCATCCTGATCTACCTGCTGAGCCCCGATGGACT
CTTCCTGGACTACTACAACCGCATGAAGAGCAGCGAGCAGATCGCCGACAGCGTCAGGAACCACATGAGGAGCTACCAGA
GGCTCTGA

Alignment

ORF - retro_olat_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 71.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAVTFAIGGALLGVMKYFKKEKEELLEKERNKSIGRPALG-GPFSLVDHNNKPTKSQDFLGQWVLLYFGF
          L.V....GG.LLG...Y...EK.......R.......ALG.G.FSLVDH.......QDFLG.WVLLYFGF
Retrocopy LLVSLLFGGGLLGAWAYVYWEKQQRRWQQRTEQLRKVALGQGTFSLVDHTGRRRTKQDFLGSWVLLYFGF

Parental  THCPDICPDEIEKMIEVVDEIDKIQSLPNLTPLLITIDPERDTPEAMAAYVKEFSPKLIGLTGSTAQIEE
          THCPDICPDE..K....V...D...SLP...PL.IT.DPERD...A.A.YVK.F.P.LIGLTG.......
Retrocopy THCPDICPDELDKLSAAVAVLDQDASLPPVQPLFITVDPERDGVPALARYVKDFHPRLIGLTGTPEEVKH

Parental  VSRAYRVYYSQGPKDEDNDYIVDHTIIMYLIGPDGEFVEYFGQNKRGVEISNSIAAHMRKHRK
          ..R.YRVY.S.GPKD.D.DYIVDH.I..YL..PDG.F..Y....K....I..S...HMR....
Retrocopy AGRDYRVYASPGPKDQDGDYIVDHSILIYLLSPDGLFLDYYNRMKSSEQIADSVRNHMRSYQR

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

1 EST(s) were mapped to retro_olat_14 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AM350787	3136	3331	100	195	0	195

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_14 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14 ,