RetrogeneDB ID: retro_gacu_1

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXI:9503049..9504150(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000011189
• 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_1
ATGGACTCCTGGATCTTGCCGTCGTCCCCTCCCAACCTGTCGGAGCACCTGATGTACGACAGCTTCGAGCCGGACCTCCA
CGGGAACTACACGGACCACAGCTTCAATAAAACCAGCACGGTGGTCATCACCTGCCTGTACTTTTTGGTCTGCACGGTGG
GACTGTGCGGGAACACCCTGGTCATCTACGTGATCCTGCGCTACGCCAAGATGAAGACGGTTACCAACATCTACATCCTC
AACCTGGCGGTGGCCGACGTGCTGTTCATGCTGGGCCTGCCGTTCATCGCCATCCAGCTGGCGCTGGTCCACTGGCCGTT
CGGCCCCGTGCTCTGCAGGGTGGTGATGGCCCTGGACTCCCTCAACCAGTTCACCTCCATCTTCTGCCTGATGGTCATGA
GCATCGACCGCTACCTGGCCGTGGTGCATCCCATCAAGTCCACAAAGTGGCGCAAGCCGCGCATGGCCAAGACTATCAAC
CTAGCGGTGTGGGGGTCGTCGCTGATGGTCAACCTTCCCATCGTCATTTACAGCGGAGTCATCACAAAGCACGACGGCTG
CTTCTGCACCATTGTGTGGCCGGAGCCTCAAGAGGCTTACTACACCGCGTTCATGTTCTACACCTTCATCCTGGGCTTCT
TCCTGCCCCTCATGGTCATCTGCCTCTGCTACTTGTTCATCATCTTCAAGGTGAAGTCCTCGGGCATCCGCGTGGGCTCG
TCCAAGAGGAAGCGCTCGGAGAGGAAGGTGACTCGCATGGTGTCCATCGTGGTGGCCGTGTTCGTCTTCTGCTGGCTGCC
CTTCTACGTCTTCAACGTCACCTCGGTGACGGGGACCATCAGCACCACCCCCATCCTCAGGAGCACCTTCGCCTTTGTGG
TGGTCCTGGGATACGCCAACAGCTGCGCCAACCCCATCCTCTACGCCTTCCTGTCGGAGAACTTCAGGAAGAGCTTCCAG
AATGTTCTGTGTCTCAAGAAGGTGGGCGGGCTGGACGAGGCCGATCGCAGCGACAGCCGGCAGGACAAGTCTCGCATGAT
AAACGACCCCACGGACACCCAGAGTACTCTGCTGAACGGGGACCTGCAGACCAGCATCTGA

Alignment

ORF - retro_gacu_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.69 %
• Parental protein coverage: 90.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQGSSTLMTAVVSLSVFVVGLTGNTLAIYVVLRHAKMKTVTNIYILNLAVADELYIIGLPFLTTQNVLSY
          F...ST.........V..VGL.GNTL.IYV.LR.AKMKTVTNIYILNLAVAD.L...GLPF...Q..L..
Retrocopy FNKTSTVVITCLYFLVCTVGLCGNTLVIYVILRYAKMKTVTNIYILNLAVADVLFMLGLPFIAIQLALVH

Parental  WPFGSFLCRVVMTADSMNQFTSIFCLTIMSIDRYLAVVHPISSTKWRHPRVAKVVSAAVWVVSFVVVLPV
          WPFG..LCRVVM..DS.NQFTSIFCL..MSIDRYLAVVHPI.STKWR.PR.AK....AVW..S..V.LP.
Retrocopy WPFGPVLCRVVMALDSLNQFTSIFCLMVMSIDRYLAVVHPIKSTKWRKPRMAKTINLAVWGSSLMVNLPI

Parental  VIFSDVQDTFNS--CNMNWPEPKHVWSTAFILYTATVGFFGPLLIICLCYLLIVIKIKSSGARAGFTKRR
          VI.S.V........C...WPEP.....TAF..YT...GFF.PL..ICLCYL.I..K.KSSG.R.G..KR.
Retrocopy VIYSGVITKHDGCFCTIVWPEPQEAYYTAFMFYTFILGFFLPLMVICLCYLFIIFKVKSSGIRVGSSKRK

Parental  RSERKVTRMVVVIVVVFVLCWLPFFIINIVNLVVIIPESSVTAGIYFFAVILSYANSCANPVLYGFLSDN
          RSERKVTRMV...V.VFV.CWLPF...N.......I...........F.V.L.YANSCANP.LY.FLS.N
Retrocopy RSERKVTRMVSIVVAVFVFCWLPFYVFNVTSVTGTISTTPILRSTFAFVVVLGYANSCANPILYAFLSEN

Parental  FRQSFRKVLCVRSVRCKTNGVNDGDPSAPRTEKS
          FR.SF..VLC......K..G....D.S..R..KS
Retrocopy FRKSFQNVLCLK----KVGGLDEADRSDSRQDKS

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_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_1 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_9

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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,