RetrogeneDB ID: retro_gacu_8

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXXI:11642787..11643768(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000005570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: mc5ra
• Ensembl ID: ENSGACG00000003733
• Aliases: None
• Description: melanocortin 5a receptor [Source:ZFIN;Acc:ZDB-GENE-021223-3]

Sequence

>retro_gacu_8
ATGAACAGCACGCAGAGCGGTGGGTTGATCCAAGGCTACCACAACAGGAGCGCCTCAGGCGTCTCGCCACCCGACAACGA
TCTAGCGGCCGAGGGGAAAGACGCGTCGGCGGGATGCTACGAGCAGCTGCTCATTTCCACGGAGGTCTTCCTCACTCTGG
GCATCATCAGCCTGCTGGAGAACATCCTGGTCGTCGCCGCCATCGTCAAAAACAAGAACCTCCACTCGCCCATGTACTTC
TTCATCTGCAGCCTGGCCGTCGCCGACATGCTCGTCAGCGTCTCCAACGCCTCCGAGACCATCGTCATCGCGCTCATCGC
CGGCGGCACCCTGACCATCCCGGTGGCTCTGATCCGGAACATGGACAACGTGTTTGACTCGATGATCTGCAGCTCTCTGC
TGGCCTCCATCTGCAGCCTGCTGGCCATCGCCGTGGACCGCTACATCACCATCTTCTACGCGCTGCGCTACCACAACATC
GTCACCCTGCGGCGCGCCACGCTGGTCATCGGCAGCATCTGGACGTGCTGCACGGTGTCCGGCATCCTCTTCATCATCTA
CTCGGAGAGCACCTCGGTGCTCATCTGCCTCATCACCATGTTCTTCACCATGCTGGTGCTCATGGCGTCGCTGTACGTCC
ACATGTTCCTGCTGGCCCGTCTGCACATCAAGCGGATCGCGGCGCTGCCGGGCCACGCGCCCATCCACCAGCGCGCCAAC
ATGAAGGGCGCCATCACCCTCACCATCCTCCTCGGGGTGTTTGTGGTGTGCTGGGCGCCTTTCTTCCTCCACCTCATCCT
CATGATCACCTGCCCCAGGAACCCCTACTGCACCTGCTTCATGTCCCACTTCAACATGTACCTCATCCTCATCATGTGCA
ACTCCGTCATCGACCCCATCATCTACGCCTTCCGCAGCCAGGAAATGAGGAAGACCTTCAGAGAAATCTTCTGCTGCTCG
CACGCGCTGCTCTTCGTGTGA

Alignment

ORF - retro_gacu_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.35 %
• Parental protein coverage: 89.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAYSYHHQNYTPVPPLHPDKTGTSKPAAC---EQVHIAIEVFLILGIISLLENILVITAIVKNKNLHSPM
          L...YH......V.P...D.....K.A.....EQ..I..EVFL.LGIISLLENILV..AIVKNKNLHSPM
Retrocopy LIQGYHNRSASGVSPPDNDLAAEGKDASAGCYEQLLISTEVFLTLGIISLLENILVVAAIVKNKNLHSPM

Parental  YFFVCSLAVADMLVSVSNAWETIVIYLLNNRQLVVEDHFIRQMDNVFDSMICISVVASMCSLLAIAVDRY
          YFF.CSLAVADMLVSVSNA.ETIVI.L.....L......IR.MDNVFDSMIC.S..AS.CSLLAIAVDRY
Retrocopy YFFICSLAVADMLVSVSNASETIVIALIAGGTLTIPVALIRNMDNVFDSMICSSLLASICSLLAIAVDRY

Parental  VTIFYALRYHNIMTVRRAGCIIGGIWTFCTGCGIIFIIYSDTTPVIICLVSMFFAMLVIMASLYSHMFML
          .TIFYALRYHNI.T.RRA...IG.IWT.CT..GI.FIIYS..T.V.ICL..MFF.MLV.MASLY.HMF.L
Retrocopy ITIFYALRYHNIVTLRRATLVIGSIWTCCTVSGILFIIYSESTSVLICLITMFFTMLVLMASLYVHMFLL

Parental  ARSHVKRIAALPGYNSIHQRTSMKGAITLTILLGIFIVCWAPFFLHLILMISCPRNLYCVCFMSHFNMYL
          AR.H.KRIAALPG...IHQR..MKGAITLTILLG.F.VCWAPFFLHLILMI.CPRN.YC.CFMSHFNMYL
Retrocopy ARLHIKRIAALPGHAPIHQRANMKGAITLTILLGVFVVCWAPFFLHLILMITCPRNPYCTCFMSHFNMYL

Parental  ILIMCNSVIDPLIYAFRSQEMRKTFKEIICC
          ILIMCNSVIDP.IYAFRSQEMRKTF.EI.CC
Retrocopy ILIMCNSVIDPIIYAFRSQEMRKTFREIFCC

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_8 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_17

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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,