RetrogeneDB ID: retro_gacu_11

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: scaffold_47:436205..437216(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000000775
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSTR5 (1 of 2)
• Ensembl ID: ENSGACG00000018944
• Aliases: None
• Description: somatostatin receptor 5 [Source:HGNC Symbol;Acc:11334]

Sequence

>retro_gacu_11
GCCAGTAAAATCATCATTCCATCCATCTATGCTCTTGTCTGCTGTGTAGGTCTAACTGGCAATGCCATGGTCATCTATGT
CATACTGAAATATGCCAAAATGAAAACAGCCACTAACATTTACATCCTAAACCTAGCGATTGCTGATGAGTTGTTTATGT
TAAGTGTTCCTTTTCTGGCCACTTCAGCTGCCATCCGTCATTGGCCCTTCGGGTCGCTGATGTGTAGGCTGGTGCTGAGT
GTAGACGGTATCAACATGTTTACATCAATCTTCTGCCTGACTGTGTTGAGTGTTGACCGATACGTAGCAGTTGTACACCC
TATAAAGGCTGCCCGCTACCGCAGACCGACAGTCGCGAAAGTAGTCAATGTGTGTGTATGGGGGCTCTCACTCATAGTCA
TCCTGCCCATCATCATCTTCGCAGACACTGTCCCTGCGCAGGACGGTGGTGTGGATTGTAACTTCTTGTGGCCTGAATCA
GCGTGGTCACAAGCATTTATGGTCTATACCTTTCTGTTGGGGTTTCTTCTGCCGGTTGGAGCAATATGCTTATGCTACTG
TTTAATGGTGGCCAGGATGCGAGCAGTGGGGCTGAAAGCAGGCTGGCTCCAACGGCGGCGCTCGGAGAAGAAGATAACCC
GCATGGTGCTGCTAGTCGTTGCAGTGTTTGTTCTCTGCTGGATGCCCTTCTATATTGTCCAGCTTGTCACCGTTTTCCAC
CGGCCCCCAGACCCAATGGTCACTCAGCTTTTTGTCATCCTCAGCTACGCCAACAGTGGCGCCAATCCTATTCTGTACGG
CTTTGTGTCTGACAATTTCCGCCGTTCGTTCCAGCGCATTGTGTGTTTCCGGTGGGTGGAGTCTGGGTTGGATGCGGAAC
AGGTGGATTACTGTGCTGTAGCTTTAAAGAGACAAGAAACTTGTAGCCCTCTGGATTTTCCCAAGGACTGTATGGCTTCT
GATATTGTGTTTCGCAATGGGACATGTACCTCTCGTACAACCACTGTGTAA

Alignment

ORF - retro_gacu_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.71 %
• Parental protein coverage: 84.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSTLMTAVVSLSVFVVGLTGNTLAIYVVLRHAKMKTVTNIYILNLAVADELYIIGLPFLTTQNVLSYWPF
          .S..........V..VGLTGN...IYV.L..AKMKT.TNIYILNLA.ADEL.....PFL.T......WPF
Retrocopy ASKIIIPSIYALVCCVGLTGNAMVIYVILKYAKMKTATNIYILNLAIADELFMLSVPFLATSAAIRHWPF

Parental  GSFLCRVVMTADSMNQFTSIFCLTIMSIDRYLAVVHPISSTKWRHPRVAKVVSAAVWVVSFVVVLPVVIF
          GS..CR.V...D..N.FTSIFCLT..S.DRY.AVVHPI.....R.P.VAKVV...VW..S..V.LP..IF
Retrocopy GSLMCRLVLSVDGINMFTSIFCLTVLSVDRYVAVVHPIKAARYRRPTVAKVVNVCVWGLSLIVILPIIIF

Parental  SD---VQDTFNSCNMNWPEPKHVWSTAFILYTATVGFFGPLLIICLCYLLIVIKIKSSGARAGFTKRRRS
          .D....QD....CN..WPE....WS.AF..YT...GF..P...ICLCY.L.V......G..AG...RRRS
Retrocopy ADTVPAQDGGVDCNFLWPE--SAWSQAFMVYTFLLGFLLPVGAICLCYCLMVARMRAVGLKAGWLQRRRS

Parental  ERKVTRMVVVIVVVFVLCWLPFFIINIVNLVVIIPESSVTAGIYFFAVILSYANSCANPVLYGFLSDNFR
          E.K.TRMV...V.VFVLCW.PF.I...V......P...VT.....F....SYANS.ANP.LYGF.SDNFR
Retrocopy EKKITRMVLLVVAVFVLCWMPFYIVQLVTVFHRPPDPMVT---QLFVIL-SYANSGANPILYGFVSDNFR

Parental  QSFRKVLCVRSV
          .SF....C.R.V
Retrocopy RSFQRIVCFRWV

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_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_11 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000018944	2 retrocopies	retro_gacu_1, retro_gacu_11 ,
Gadus morhua	ENSGMOG00000018538	1 retrocopy	retro_gmor_13,
Oreochromis niloticus	ENSONIG00000017693	1 retrocopy	retro_onil_17,
Tetraodon nigroviridis	ENSTNIG00000014076	1 retrocopy	retro_tnig_9,
Xiphophorus maculatus	ENSXMAG00000012731	1 retrocopy	retro_xmac_18,