RetrogeneDB ID: retro_tnig_17

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: Un_random:89458141..89459113(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000008689
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: mc5ra
• Ensembl ID: ENSTNIG00000013316
• Aliases: None
• Description: melanocortin 5a receptor [Source:ZFIN;Acc:ZDB-GENE-021223-3]

Sequence

>retro_tnig_17
ATGAACGCCACAGATCCTCCTGGGCTCATCCAGGACTACAACAATGGGAGCCAAACACTGGAGGCAGACTTTCCAGACGA
GGAGGAGAAGGAGTCGTCGGCAGGATGCTACGAGCAGCTGCTGATCTCCACCGAGGTGTTTCTGACTCTGGGCATCGTCA
GCCTGCTGGAGAACATCCTGGTGGTCGCTGCTATAGTCAAGAACAAGAACCTCCACTCGCCCATGTACTTTTTCATCTGC
AGCCTGGCCGTGGCCGACATGCTGGTGAGCGTCTCCAACGCCTCGGAGACTATCGTCATCGCGCTCATCAACGGGGGCAC
GCTGACCATCCCGGCAAGGCTGATCAAAAGCATGGACAACGTCTTTGACTCCATGATCTGCAGCTCTCTGCTGGCGTCCA
TCTGCAGCCTGCTGGCCATCGCCGTCGATCGTTACATCACCATCTTCTACGCCCTGCGCTACCACAACATCGTCACCCTG
CGCAGAGCCTCGCTGGTCATCAGCAGCATCTGGACCTGCTGCACCGTGTCCGGCGTCCTCTTCATCATCTACTCGGAGAG
CACCACCGTGCTCATCTGCCTCATCACCACCTTCTTCACCATGCTGGTGCTCATGGCCTCTCTGTACGTGCACATGTTTC
TGCTGGCGCGCCTGCACATGAAGCGGATCGCGGCGATGCCGGGCAACGCGCCCATCCACCAGAGGGCCAACATGAAGGGC
GCCATCACCCTCACCATCCTGCTGGGAGTGTTTGTGGTGTGCTGGGCACCCTTCTTCCTCCACCTCATCCTCATGATCAC
CTGCCCCAAGAACCCGTACTGCACCTGCTTCATGTCGCACTTCAACATGTACCTCATCCTCATCATGTGCAACTCCGTCA
TCGACCCCATCATCTACGCCTTCCGCAGCCAGGAGATGAGGAAGACCTTCAAGGAGATCTTCTGCTGCTCCCAGGCGCTG
CTGTGCATGTGA

Alignment

ORF - retro_tnig_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 85.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPLPKNKTAAC-EQLHIAIEVFLILGIISLLENILVITAIVKNKNLHSPMYFFVCSLAVADMLVSVSNA
          P....K...A.C.EQL.I..EVFL.LGI.SLLENILV..AIVKNKNLHSPMYFF.CSLAVADMLVSVSNA
Retrocopy PDEEEKESSAGCYEQLLISTEVFLTLGIVSLLENILVVAAIVKNKNLHSPMYFFICSLAVADMLVSVSNA

Parental  WETIIIYLLNNKQLVVEDHFIQQLDNVFDSMICISVVASMCSLLAIAVDRYVTIFYALRYHNIMTVRRAG
          .ETI.I.L.N...L......I...DNVFDSMIC.S..AS.CSLLAIAVDRY.TIFYALRYHNI.T.RRA.
Retrocopy SETIVIALINGGTLTIPARLIKSMDNVFDSMICSSLLASICSLLAIAVDRYITIFYALRYHNIVTLRRAS

Parental  CIIGGIWTFCTGCGIVFIIYSEKTPVIICLVSMFFAMLLIMASLYSHMFMLARSHVKRIAALPGSSSIQQ
          ..I..IWT.CT..G..FIIYSE.T.V.ICL...FF.ML..MASLY.HMF.LAR.H.KRIAA.PG...I.Q
Retrocopy LVISSIWTCCTVSGVLFIIYSESTTVLICLITTFFTMLVLMASLYVHMFLLARLHMKRIAAMPGNAPIHQ

Parental  RANMKGAITLTILLGIFIVCWAPFFLHLILMISCPRNVYCVCFMSHFNMYLILIMCNSVIDPLIYAFRSQ
          RANMKGAITLTILLG.F.VCWAPFFLHLILMI.CP.N.YC.CFMSHFNMYLILIMCNSVIDP.IYAFRSQ
Retrocopy RANMKGAITLTILLGVFVVCWAPFFLHLILMITCPKNPYCTCFMSHFNMYLILIMCNSVIDPIIYAFRSQ

Parental  EMRKTFKEIICC
          EMRKTFKEI.CC
Retrocopy EMRKTFKEIFCC

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_17 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_8

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000003733	1 retrocopy	retro_gacu_8,
Oreochromis niloticus	ENSONIG00000006909	1 retrocopy	retro_onil_4,
Tetraodon nigroviridis	ENSTNIG00000013316	1 retrocopy	retro_tnig_17 ,