RetrogeneDB ID: retro_onil_57

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831432.1:546827..547639(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM92A1
• Ensembl ID: ENSONIG00000002446
• Aliases: None
• Description: None

Sequence

>retro_onil_57
ATGAGCCGTACGCCTGACACAAGCACGAGGGATAACCAAACAAGGAGGATCCAATGGAACATCACCAATGTGGAGAAACA
TTTTGGACAGATGTGCCAACTCTTTGCTGCCTTTGTCAGTAAGACAGCCAAGGTACGAAACAAGGCAGACCTTCTGGTCC
GGGAAATTAGCCTGTATGCAGACACCGAAACACCAAGCCTTAAGAGGGGGTTGAAGCAGTATGCTGACCATCTGGCCAAG
ATTCAAGATTATCGTCAAGCTCAGGTGAAATAACTTGAATCTAAAATCATAGAGCCATTAAAAAAAGCTGTAGTGAAATG
GAAAAGGGAGGATCTGAAGACTACTCAGAGTGCCAGAGACAGAGAAGCCAAACAGATGGCTCAGCTCGAGAGGACCAGGC
AGAGAAACCCCTCAGACATGCAGATCATTTCTCAGGCTGAGAGTGAACTCCAGAGAGCCACCATGGATGCCACATGGACC
ACGAAGCAACTGGAGGAGACCATCGATGAGTTTGAGAGGCAGAAGATCCAAGACATCAAGAAAGTCTTTTGTGAGTTTGT
GACAGTGGAAATGTCATTCCACGCCAAGGCTTTGGAGGTGTACACCCTGGCCTACCAAAGCATTCAAAGTGTGGACAAGG
AGGAGGACAAGGAGGTGTTCAGGAGTTCTCTGCACCCCCCCCCCCCCCCGGATATAAGTCATGCTTAGACATAGTGTGAG
CTAATTCCACAACTTCCCTTGATCAGACCGGGTCCTTCCTGAACTCATCAGGGACATTACAGCAACAAAGAGCTGGTAGT
CGTCAGACGAGA

Alignment

ORF - retro_onil_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.85 %
• Parental protein coverage: 90.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRTPDARARDNQTRRIQENITNVEKHFGQMCQLFAAYVRKTAKVRDKADLLVQEIGLYADTETPSLKRG
          MSRTPD...RDNQTRRIQ.NITNVEKHFGQMCQLFAA.V.KTAKVR.KADLLV.EI.LYADTETPSLKRG
Retrocopy MSRTPDTSTRDNQTRRIQWNITNVEKHFGQMCQLFAAFVSKTAKVRNKADLLVREISLYADTETPSLKRG

Parental  MKQYADHLAKIQDYRQAQVERLESKIIEPLKSYGAVVKRKREDLKTTQSARDREAKQMAQLERTRQRNPS
          .KQYADHLAKIQDYRQAQV..LESKIIEPLK...AVVK.KREDLKTTQSARDREAKQMAQLERTRQRNPS
Retrocopy LKQYADHLAKIQDYRQAQVK*LESKIIEPLKK--AVVKWKREDLKTTQSARDREAKQMAQLERTRQRNPS

Parental  DRQIISQAESELQRATMDATRTTKQLEETIDEFERQKIQDIKKIFCEFVTVEMSFHAKALEVYTLAY---
          D.QIISQAESELQRATMDAT.TTKQLEETIDEFERQKIQDIKK.FCEFVTVEMSFHAKALEVYTLAY...
Retrocopy DMQIISQAESELQRATMDATWTTKQLEETIDEFERQKIQDIKKVFCEFVTVEMSFHAKALEVYTLAYQSI

Parental  QSIQSVDEEE-DLEVFRSSLHPPDYQSRLDIVRANSKTSLDRTGSFLNSSGTLQQQRAGSRQTR
          QS.......E.....F........Y.S.LDIV.ANS.TSLD.TGSFLNSSGTLQQQRAGSRQTR
Retrocopy QSVDKEEDKE<GVQEFSAXXXXXGYKSCLDIV*ANSTTSLDQTGSFLNSSGTLQQQRAGSRQTR

Legend:

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

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_57 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_57 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57 ,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235, retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,