RetrogeneDB ID: retro_gacu_4

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXIX:11698896..11700207(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000010047
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gpr22
• Ensembl ID: ENSGACG00000019247
• Aliases: None
• Description: G protein-coupled receptor 22 [Source:ZFIN;Acc:ZDB-GENE-041210-48]

Sequence

>retro_gacu_4
ATCCTTCGCTGCCCTGAACAAGAAGCCACGATGAGCAACGTCACGGTCACCGACAACACTGAGCCCATCAGCCGCACCAT
GAGTCCGGCAAGCCCCAGCCCGTATCCCTATCCTGTTAGTTTCCAGGTCTCCCTGACATGCTTCCTCATGCTGGAAATCC
TCCTGGGAATGAGCTCCAACCTCACTGTGCTCGCCCTTTACTGTATGAAGTCGAACCTCATTAGCTCTGTCAGTAACATT
GTCACCATGAACCTCCATGTGCTGGATGTGCTCATCTGTGTGTGCTGCATCCCCCTCACCATTGTGGTGGTGTTGCTCTC
GCTGGAGGGGGACACTGCGCTGGTCTGCTGCTTCCATGAAGCCTGCGTCTCCTTCGCTAGCGTCGCCACTGCCGCTAACG
TGCTGGCCATCACCCTCGACCGCTACGACATCTCGGTCAAGCCGGCCAACCGGGTACTGACCATGGGCCGCGCCCTGACC
CTGCTGTCTGCCATTTGGGTGCTGTCCTTTGTCAGTTTCCTCGTGCCCTTTATTGAGGTGGGCTTCTTCGCCCAGGGACA
AGCCGATCTGAACCAGACAGCGGTGGAGAACGTGGTCCACACTAACCAGTACTACACAGAGCTCGGCCTCTATTACCATC
TGCTCGCTCAGATTCCGATTTTCTTCTTAACCGCCGTGGTCATGCTCATCACCTACTCAAAGATCCTGCAGGCGCTCAAC
ATTCGCATTGGCACACGGTTCCACGCCTCACAGAAGAAGAAGGCTCGCAGGAAAAAAAGCCCATCCATGACGGCCATGAA
GACACAGCACGAGGCCACGGATGCTTCCCAGAGCAGCGGCAGCCGCAACCCCACCCTGGGGATGCGCACCTCCGTCTCCG
TCATCATCGCCTTGCGCAGGGCGGTCAAGCGCCACCGAGAAAGGCGGGAACGCCAAAAGAGGGTCTTCAGAATGTCCCTC
CTGATTGTGTCTACCTTCATGCTGTGCTGGACGCCAATCACAGTGCTCAACACGATCATCCTGAGTGTGGGCCCCAGTGA
CCTGATGGTCAAGTTGAGACTGGGCTTCCTGGTGATGGCTTATGGGACCACTATCTTTCACCCTCTACTCTATGCCTTCA
CCAGGCAGAAGTTCCAGAAAGTCTTGAAAAGCAAGATGAAGAAGCGAGTGGTGTCGATCATTGAGGCCGATCCTACCCCG
AACAATGCCATCATCCACAACTCCTGGATCGACCCAAAGAGGAATAAAAAGGTGACATTTGAGGACAAAGACGCCCAACA
GAAATGTCTGTCTTCTGAGGACGTGGCGTGA

Alignment

ORF - retro_gacu_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69. %
• Parental protein coverage: 97.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAVSNMTVLDTAD--SQDLDTTSDKPI-YPISFQVSLTGFLLLEIVLGLSSNLTVLVLYCMKQNLISSVS
          A..SN.TV.D.....S......S..P..YP.SFQVSLT.FL.LEI.LG.SSNLTVL.LYCMK.NLISSVS
Retrocopy ATMSNVTVTDNTEPISRTMSPASPSPYPYPVSFQVSLTCFLMLEILLGMSSNLTVLALYCMKSNLISSVS

Parental  NIITMNLHVVDV-VCVCCIPLTAVVVLFPLETDTAMISCFHEACVSFTSVATAVNVLAITVDRYDISVRP
          NI.TMNLHV.DV..CVCCIPLT.VVVL..LE.DTA...CFHEACVSF.SVATA.NVLAIT.DRYDISV.P
Retrocopy NIVTMNLHVLDVLICVCCIPLTIVVVLLSLEGDTALVCCFHEACVSFASVATAANVLAITLDRYDISVKP

Parental  ASRVLTKGRAVALLGCIWALSFGSFLVPFMEVSFFINSVPDLVNGTVVVTVAHPNEYYTEQGLYYHLVAQ
          A.RVLT.GRA..LL..IW.LSF.SFLVPF.EV.FF.....DL.N.T.V..V.H.N.YYTE.GLYYHL.AQ
Retrocopy ANRVLTMGRALTLLSAIWVLSFVSFLVPFIEVGFFAQGQADL-NQTAVENVVHTNQYYTELGLYYHLLAQ

Parental  IPIFFFTALVMLVTYYKILQALNIHIGAHFQSHLPSKKQKRKNTLCLSTATQAESTDASRSSTGVRAGGN
          IPIFF.TA.VML.TY.KILQALNI.IG..F......K....K........TQ.E.TDAS.S..G.R...N
Retrocopy IPIFFLTAVVMLITYSKILQALNIRIGTRFHASQKKKARRKKSPSMTAMKTQHEATDASQS-SGSR---N

Parental  PPLDMHVSVSVIITLRRAVRRHRERRKRQERVFRVSLLIIATFLLCWTPITVLNTIILSTGPSGLTVLLR
          P.L.M..SVSVII.LRRAV.RHRERR.RQ.RVFR.SLLI..TF.LCWTPITVLNTIILS.GPS.L.V.LR
Retrocopy PTLGMRTSVSVIIALRRAVKRHRERRERQKRVFRMSLLIVSTFMLCWTPITVLNTIILSVGPSDLMVKLR

Parental  LGFLVMAYGTTIFHPLLYAFTRQKFQKVLKSNMKKRVGSVVEA--TPNNVVIHKLWIDPRRNKKVTVKDM
          LGFLVMAYGTTIFHPLLYAFTRQKFQKVLKS.MKKRV.S..EA..TPNN..IH..WIDP.RNKKVT..D.
Retrocopy LGFLVMAYGTTIFHPLLYAFTRQKFQKVLKSKMKKRVVSIIEADPTPNNAIIHNSWIDPKRNKKVTFEDK

Parental  EAILKCLSS
          .A..KCLSS
Retrocopy DAQQKCLSS

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_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_4 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_15

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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	ENSGACG00000019247	1 retrocopy	retro_gacu_4 ,
Oreochromis niloticus	ENSONIG00000014203	1 retrocopy	retro_onil_13,
Tetraodon nigroviridis	ENSTNIG00000007247	1 retrocopy	retro_tnig_15,