RetrogeneDB ID: retro_onil_31

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831178.1:4336672..4338172(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020447
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNS1
• Ensembl ID: ENSONIG00000005340
• Aliases: None
• Description: None

Sequence

>retro_onil_31
ATGGGGTATGGGCAAATCCTCCACCGGCGTGGGGATGAGGAGGACCAGGTCCACCTCAATGTGGGAGGGGTACGGCATGA
ACTGGATCCTGATATGGTGCTCCGCTTTCCTCACACACGTTTGGCTCGTCTGCTGTGCTGCCAGAGCGAGGCGGCAATCC
TGGAGCTGTGTGACGACTACAGCCCGGCTGAGAAGGAGTACTACTTTGACAGGAATCCTCGGGTTTTCCTCTGCGTGCTT
AACTTTTACCACACAGGACAAATCCACATGATGGAGGAGCTGTGCGTTTTTTCTTTCTGCCAGGAGATTGAGTACTGGGG
CATCAAGGAGCTCCACCTCAGCCCCTGCTGCAGTAACTGGTACCACGAGAGGAAGGAGTACATCGAGGACAGAGACTGGG
ACATCGGGAGCGAAGACCAGCAGGAGCCGAGCTTCGACTCCTCGTTTGAGGAGCTCTCTGCTCTCGATAAAGACCTCGCC
AAGTTTAAAGGTGCCTGGTGTGCAGAAATTCGCAGCTACGTGTGGCTCAGACTGGAGGATCCGGGTCACTCGAGAGCCTC
GAAGATCATTGCTGTGGCTTCCCTCAGCGTGGTGTTGACCTCCATCGTTGCCATGTGTGTTCACAGCATGCCAGAGTTTC
AGCGTGTGGATGACAGTGACAGGCCCATCGAGGACCCCGTGCTCACTAGACTGGAAGAGGTTTGCATCGCCTGCTTCTCC
GCAGAGTTTATAATCAGGTTAATCGTCGCGCCCTCCCGACGGAAGTTTCTCGGAAACCCCTTGAACATAATCGACGCCGC
TTCGATTTTGCCATTTTATGCCACTTTAGCTCTGGAGACAGCCGACGAGGAGAGCGCCGAGGAGAATGAGGACATAGAAA
ACGTGGGGAAAGTGGTGCAGGTTCTGCGCCTCATGCGGGTTCTCAGAATCCTCAAACTGGCTCGCCACTCCATCGGACTG
CGAGCGCTGGGGGCCACCGTCCGCCACAGCTACCAGGAGGTGGGCCTGCTCCTTCTCTTCCTCTCAGTGGGAATCTCCAT
CTTTTCTGCTCTCATCTACTTCGCGGAGAAGGAAGAGAAGCAAACAGATTTGGGGACAATACCTTCAGGTTGGTGGTGGG
CCACAATCACCATGACCACAGTCGGCTACGGGGACACCTGCCCCGTGACGGTGGCGGGGAAGATTGTGGCCACCGTGTGT
ATCATCTGTGGCCTGCTAGTGGTGGCTCTTCCCATCACCATCATCTTTAACAAGTTTTCAAAGTACTATCAAAGAAACAA
AGCCATGGAGGGACAGTGCATCACCAAGCCTGAAAGACAAGACCCAGAACTCCCTCATTACAACATCAGGGAACTGTTAA
CGGGAAGCGTGTACCCCTTTATAGGAAGCATCGCCTTTAGGAACAGTGGGAGCAGCGGAGGGGACGATACGGACGCCTCC
AGTCTCCAGGACATCGAGGTGTACGATAATGACGCTTGTGAAAATGGAGCAGCCAAATGA

Alignment

ORF - retro_onil_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.22 %
• Parental protein coverage: 81.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEGLVHVNVGGLKRSLCSSTLKKFPDTRLGKLLACDSEEAILQVCDDYDVQEKEFYFDRNPGLFPYVLHF
          .E..VH.NVGG....L.......FP.TRL..LL.C.SE.AIL..CDDY...EKE.YFDRNP..F..VL.F
Retrocopy EEDQVHLNVGGVRHELDPDMVLRFPHTRLARLLCCQSEAAILELCDDYSPAEKEYYFDRNPRVFLCVLNF

Parental  YQTGKLHIMEELCVFSFSQEIEYWGINEFFLDSCCSYRYHDRKLESSRHRSWD---DESDASSVDTSVDE
          Y.TG..H.MEELCVFSF.QEIEYWGI.E..L..CCS..YH.RK.E....R.WD.........S.D.S..E
Retrocopy YHTGQIHMMEELCVFSFCQEIEYWGIKELHLSPCCSNWYHERK-EYIEDRDWDIGSEDQQEPSFDSSFEE

Parental  ISDLNKDMQHFQEVRYGNIRKCLWLTLENPGYSIPSKLFSLLSIGVVLTSIATMCINSMPEYQTFDSDGK
          .S.L.KD...F.......IR...WL.LE.PG.S..SK.....S..VVLTSI..MC..SMPE.Q..D....
Retrocopy LSALDKDLAKFKGAWCAEIRSYVWLRLEDPGHSRASKIIAVASLSVVLTSIVAMCVHSMPEFQRVDDSDR

Parental  LIEEPTMQALEVFCSCWFTFEVVTRLLLAPNRKKFFHHPLNIIDMVSVVPIYVTLVFDVTVGSESE----
          .IE.P....LE..C...F..E...RL..AP.R.KF...PLNIID..S..P.Y.TL..........E....
Retrocopy PIEDPVLTRLEEVCIACFSAEFIIRLIVAPSRRKFLGNPLNIIDAASILPFYATLALETADEESAEENED

Parental  LGDLGRLIQVFRLMRIFRVLKLARHSTGLRSLGATLRHSYREVGILLLYLAVGVSVFSGIAYTAEYEE-D
          ....G...QV.RLMR..R.LKLARHS.GLR.LGAT.RHSY.EVG.LLL.L.VG.S.FS...Y.AE.EE..
Retrocopy IENVGKVVQVLRLMRVLRILKLARHSIGLRALGATVRHSYQEVGLLLLFLSVGISIFSALIYFAEKEEKQ

Parental  VGLDTIPACWWWGTVSMTTVGYGDVVPVTVVGKLAASGCILGGTLVVALPITIIFNKFSHFYRRQKALE
          ..L.TIP..WWW.T..MTTVGYGD..PVTV.GK..A..CI..G.LVVALPITIIFNKFS..Y.R.KA.E
Retrocopy TDLGTIPSGWWWATITMTTVGYGDTCPVTVAGKIVATVCIICGLLVVALPITIIFNKFSKYYQRNKAME

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_31 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_31 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000008198	1 retrocopy	retro_apla_7,
Gasterosteus aculeatus	ENSGACG00000000019	1 retrocopy	retro_gacu_10,
Oreochromis niloticus	ENSONIG00000005340	2 retrocopies	retro_onil_31 , retro_onil_7,
Tetraodon nigroviridis	ENSTNIG00000005219	1 retrocopy	retro_tnig_1,