RetrogeneDB ID: retro_drer_14

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 4:17521938..17522805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000045555
• Aliases: sco2, si:dkey-202b22.3
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSDARG00000067593
• Aliases: None
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_drer_14
CTCTATCTCTGTCTTTGTTGTTTTTTCCAGAGGATGTTAAGACTGAGGGTATTCGACAGACATAAGAGGTTATGGAGCGT
CCTGCAGTCAACAATAAGGGGAAACAACATTTCAAATCACATCCCAAACACCACATGCAGATCTTCAGCTCCACCACATT
TATGTGCACGACAAAGAGCCTTTTACTCTCAAAACTCCCCTAAAACTCCAAATCCAGGCTCGTCCGCAGGCATCAAACTG
CGCACACGCTTGGTGGTGACGCTGCTTTTTGGAGGTGGCATCATTGGCACTTGGTGGTACGTGCATCAGGAGAAAGAAAA
GAGGATTCAGATGCAAAGACTGGAGCAGTTGCGAAAAGTGGCTCTCGGACAGGGAGATTTCCATTTGCTTGATCATACGG
GACAGCGCAGAACCAAACGAGACTTTCTAGGACACTGGGTGCTGTTATATTTCGGTTTTACCCACTGTCCTGATATCTGT
CCTGATGAGCTGGAGAAGTTGACCAGCGTGGTGCATATTTTGGATAAAGACCCAAGCTTGCCTTCTGTTCAGCCTCTTTT
CATCACTGTTGACCCAGAGAGAGATGATGTTTCTGCTATGGCCAGGTATGTGAAAGATTTTCATCCCCGTTTGGTTGGAC
TGACCGGGAGCGCGGAGGAAGTGAAGCAGGCGGGACGGGATTTTAGGGTTTACGCCAGTAATGGGCCCAAAGATGAGGAT
GGGGACTATATTGTGGATCACAGCATAGTCATCTACCTGGTCAACCCGGATGGACTGTTTATCGACTATTACAATAGGAT
GAAAAATGACACCCAGATTGCTGAGAGTATTCGCAATCACATGAAGACCTTTGTTAGATTGTTTCCT

Alignment

ORF - retro_drer_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.26 %
• Parental protein coverage: 62.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAVTFALGGGLLLAMKYFKREKEELFEKERTKSIGKPALG-GPFSLLDHNNKPSRSEDFLGRWLLIYFGF
          L.VT...GGG......Y...EKE......R.....K.ALG.G.F.LLDH........DFLG.W.L.YFGF
Retrocopy LVVTLLFGGGIIGTWWYVHQEKEKRIQMQRLEQLRKVALGQGDFHLLDHTGQRRTKRDFLGHWVLLYFGF

Parental  THCPDICPDELEKMIEAVDEIDNIDTLPDVTPLLISIDPERDTPEALAAYVKDFSPKLIGLTGTTAQIEQ
          THCPDICPDELEK....V...D....LP.V.PL.I..DPERD...A.A.YVKDF.P.L.GLTG......Q
Retrocopy THCPDICPDELEKLTSVVHILDKDPSLPSVQPLFITVDPERDDVSAMARYVKDFHPRLVGLTGSAEEVKQ

Parental  VSRAYRVYYSQGPKDEDNDYIVDHTIIMYLVGPDGQFLEYYGQNKKSSEIASSIASYMR
          ..R..RVY.S.GPKDED.DYIVDH.I..YLV.PDG.F..YY...K....IA.SI...M.
Retrocopy AGRDFRVYASNGPKDEDGDYIVDHSIVIYLVNPDGLFIDYYNRMKNDTQIAESIRNHMK

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_14 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_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,