RetrogeneDB ID: retro_onil_8

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831280.1:1625148..1626168(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020701
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gtf3ab
• Ensembl ID: ENSONIG00000014134
• Aliases: None
• Description: general transcription factor IIIA, b [Source:ZFIN;Acc:ZDB-GENE-030131-7698]

Sequence

>retro_onil_8
ATGGAAACTAAAGCGGAGTCATACAAACGTTATATCTGTTCGTTTAGCGGCTGCTCGGCTGCCTACAACAAACAGTGGAA
ACTGGACGCTCACTTGTGTAAGCACACGGGGGTGAAGCCGTACTCGTGCGAGCGCGATGGCTGCAGTAAGGCGTTCTGTA
GTAAGTACCACCTAGCGAGGCACGAGCTCAGCCACAACGGAGAGAAGCCTTTCCGGTGCACCGTGGACGGCTGCGCGGAG
GCCTTCACCACCAACGCAAACCGGGCCCGACACATCGGCCGCATCCACTGCCTGGAGCCGAGGAAATACGTCTGCAGGTT
TGAGGGCTGCGGCCTCGAGTTCAAGAAGAACAAACAGCTCAAATCTCACATGTGTGAGCAGCACACTCAGCTGCCCCCTT
ATCAGTGCATTTACGAAGGCTGCCAGATGCGATTCAGCTTCCCCAGCAAACTGAAGCGTCACGAGAAGGTGCACAGAGGG
TACCCCTGCAAAGAGGAGAGCTGCGTCTTCACGGGGAAGACCTGGACTGAGTACCTGAAGCACAGGAAGGAGCAGCACAG
AGTCACCCTGAAGTGTGAGCAGTGCAGCCGAGTGTTCAGGGACACCTGGTTTCTGCAGCAGCATCAGCGCATCCACTCTG
AAATGAGAGTGGTCCTCAAATGTCCCAGGGATACCTGTGACAGGTCGTTCACCACTGCCTTCAACCTGCAGAGCCACATC
AGCTCCTTCCACGAGGAGCGCCGGCCCTTTGTCTGCACCCACGCTGGCTGTGGGAAGACGTTCGCCATGAACCAGAGCCT
CCAGCGTCATAGCGTCGTCCACGACCCACAGAGGAAGAAGCTGAAGAAGCCAAGAGCCAAAAGATCTCTTGCTTCGAGGT
TAAGCGGTTACTGTGAAACAAAGAGAGTGGTCTACAAAATGCAAACCGAACATGCAGCGCACAGACAGTCTTCACAAGAG
AAAGCAGACCAGCCTGGGCCTTTTGAGCTGGTGTCTCTCCTACAGGACGCGTCCTTGCTG

Alignment

ORF - retro_onil_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.35 %
• Parental protein coverage: 87.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTYVCSFSDCKATFSKPWKLDAHLCKHTGLKPFSCE--SCDKSFCTRYQLTRHELSHSGEKPHKCPADGC
          K.Y.CSFS.C.A...K.WKLDAHLCKHTG.KP.SCE...C.K.FC..Y.L.RHELSH.GEKP..C..DGC
Retrocopy KRYICSFSGCSAAYNKQWKLDAHLCKHTGVKPYSCERDGCSKAFCSKYHLARHELSHNGEKPFRCTVDGC

Parental  SEAFVRNASLKNHIARVHQQQEKRFQCDHQGCEKDFSKRNQLKAHQCE-HQESLPFHCSLTGCTREFLTL
          .EAF..NA....HI.R.H........C...GC...F.K..QLK.H.CE.H....P..C...GC...F...
Retrocopy AEAFTTNANRARHIGRIHCLEPRKYVCRFEGCGLEFKKNKQLKSHMCEQHTQLPPYQCIYEGCQMRFSFP

Parental  KKLKHHEKMHEGYPCETDGCPFQGKTWSDYLKHRKE-HKDKVLCGHCNKLFSNFWFFRLHELRVHSGEKR
          .KLK.HEK.H.GYPC....C.F.GKTW..YLKHRKE.H.....C..C...F...WF...H..R.HS....
Retrocopy SKLKRHEKVHRGYPCKEESCVFTGKTWTEYLKHRKEQHRVTLKCEQCSRVFRDTWFLQQHQ-RIHSEMRV

Parental  TFPCPKEGCEKKFTRRFNLESHVLGDHEGKKPFSCAVPGCNKSFAMKESLWRHGVVHDPAKKKLKKLHPK
          ...CP...C...FT..FNL.SH....HE...PF.C...GC.K.FAM..SL.RH.VVHDP..KKLKK..P.
Retrocopy VLKCPRDTCDRSFTTAFNLQSHISSFHEERRPFVCTHAGCGKTFAMNQSLQRHSVVHDPQRKKLKK--PR

Parental  KNRPMAQR
          ..R..A.R
Retrocopy AKRSLASR

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_8 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_8 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8 ,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,