RetrogeneDB ID: retro_tnig_9

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 3:10444876..10445989(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000000288
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSTR5
• Ensembl ID: ENSTNIG00000014076
• Aliases: None
• Description: somatostatin receptor 5 [Source:HGNC Symbol;Acc:11334]

Sequence

>retro_tnig_9
ATGGACTCCTGGATCCTCCCAGCGTCTCCCCCCAACCTGTCCGACCACCTCATGTACGACGGCTTCGAGCAGCTCAACGA
GTCCCACGTCCAGGTGAACCGCACCGACCACAGCCTGAACAAGACCAGCACGGTGGTCATCACCTGCATGTACTTCCTGG
TGTGCACCGTGGGGCTCTGCGGCAACGCCCTGGTCATTTACGTCATCCTGCGCTACGCCAAGATGAAGACGGTCACCAAC
ATCTACATCCTGAACCTGGCCGTGGCCGACGTGCTCTTCATGCTGGGCCTGCCCTTCATCGCCATCCAGCTGGCGCTGGT
GCACTGGCCGTTCGGGCCCATGCTCTGCAGGGTGGTGATGACCGTCGACTCCCTCAACCAGTTCACGTCCATCTTCTGCC
TGATGGTCATGAGCATCGACCGCTATCTGGCCGTGGTGCATCCCATCAAGTCCACCAAGTGGCGGAAGCCGCGCATGGCC
AAGACCATCAACGTGGCCGTGTGGGGGGCGTCGCTGATGGTCAACCTGCCCATCGTCATCTACAGCGGGATCATCACCAA
GCACGACGGCTGCTTCTGCACCATCGTGTGGCCCGAGCCCGAGGAGGCGTACTACACAGCCTTCATGATCTACACCTTCA
TCCTGGGCTTCTTCCTGCCCCTGCTGGTCATCAGTCTCTGCTACATCTTCATCATCGTCAAGGTGAAGTCGTCCGGCATC
CGCGTGGGCTCCACCAAGAGGAAGCGCTCGGAGCGAAGAGTGACGCGGATGGTGTCCATCGTGGTGGCCGTGTTCGTCCT
CTGCTGGCTGCCGTTCTACGTCTTCAACGTCACCTCGGTGACGGGCACCATCAGCACCACGCCCGTCCTGAGGAGCACCT
TTGCTTTCGTGGTGGTGCTGGGCTACGCCAACAGCTGCGCCAACCCCATCCTCTACGCCTTCCTGTCGGAAAACTTCAAG
AAGAGCTTCCAGAACGTGCTGTGTCTGCAGAAGGTCGGCGGGCTGGACGAGGTGGAACGCAGCGACAGCCGGCAGGACAA
ATCACGCATGATTAACGACCCGACTGAGACCAGGAGCACGCTGCTGAACGGCGACCTGCAGACCAGCATCTGA

Alignment

ORF - retro_tnig_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.66 %
• Parental protein coverage: 93.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSALLTAVTYLTVFAVGLSGNTLAIYVVLRYAGMKTVTNIYILNLAIADELYIIGLPFLTAQNVLSYWPF
          .S.......Y..V..VGL.GN.L.IYV.LRYA.MKTVTNIYILNLA.AD.L...GLPF...Q..L..WPF
Retrocopy TSTVVITCMYFLVCTVGLCGNALVIYVILRYAKMKTVTNIYILNLAVADVLFMLGLPFIAIQLALVHWPF

Parental  GSFLCRVVMTADSMNQFTSIFCLTVMSIDRYLAVVHPIRSTNWRHPRVAKVVSAAVWAVSFVVVLPVVVF
          G..LCRVVMT.DS.NQFTSIFCL.VMSIDRYLAVVHPI.ST.WR.PR.AK....AVW..S..V.LP.V..
Retrocopy GPMLCRVVMTVDSLNQFTSIFCLMVMSIDRYLAVVHPIKSTKWRKPRMAKTINVAVWGASLMVNLPIVIY

Parental  SDVQETFNS--CNMIWPEPKNLWSTAFILYTATLGFFGPLLIICLCYLLIIIKVKSSGERVGVTKRRRSE
          S..........C...WPEP.....TAF..YT..LGFF.PLL.I.LCY..II.KVKSSG.RVG.TKR.RSE
Retrocopy SGIITKHDGCFCTIVWPEPEEAYYTAFMIYTFILGFFLPLLVISLCYIFIIVKVKSSGIRVGSTKRKRSE

Parental  RKVTQMVVVIVVVFVLCWLPFFIINMVNLVVIIPESSTTAGIYFFAVVLSYANSCANPVLYGFLSDNLKQ
          R.VT.MV...V.VFVLCWLPF...N.......I...........F.VVL.YANSCANP.LY.FLS.N.K.
Retrocopy RRVTRMVSIVVAVFVLCWLPFYVFNVTSVTGTISTTPVLRSTFAFVVVLGYANSCANPILYAFLSENFKK

Parental  SFKKVLCVRSVRSAGGLE---PRQDAARRPHSRESSKS
          SF..VLC...V......E....RQD..R.........S
Retrocopy SFQNVLCLQKVGGLDEVERSDSRQDKSRMINDPTETRS

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_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_9 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_1

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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,