RetrogeneDB ID: retro_ttru_378

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2071:87520..88062(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SNX15
• Ensembl ID: ENSTTRG00000000324
• Aliases: None
• Description: sorting nexin 15 [Source:HGNC Symbol;Acc:14978]

Sequence

>retro_ttru_378
CCGCAGAAAGGAGGGGCGTGGAGGGGAGGGGCCTCGACGTGTTGGACGTGCCAACGGACCATCCCCCACGCCACGCCCTC
ACCATCCAGACCTGCCATCTTTAACTGTGGGAGCACCAAGGAGGCGTCCCGTGCCCCTGCCGAGCCCCGCACACCAAGAC
TGAACTTGCCCTCTTGGACCCCCTTTCCAAGGAAGAAGTCTCAGGCCTCAGTCCTACCTGCATAAGTGAGTTGGTATTGA
TGCAGAGTCCTCAAGGCTGCACCAGGGACCCTGGGAAACAGGAAGGCAGGGAGAGGAAAAGGAAGGAGGGCCCACCACCA
CCTTTCTGAGCCAAGCTACAGAGCTCATCACCCAGGGCTGCGGGAGGAGAAGGCAAGCACCTACCCTGCAGCTCTGCAGG
GTTACCGGGATGGGGTGCACATCCTGCTTCAGGGAGATCCCAGTGACCCATCCCCTGCCCTCAGGGAGGGTGTGAGGAAG
GCAGCCAACTAGCTGAAGCGTCAGAGGCAATCCTGCACCTGTACCTGTCCTAACTCCTGCCT

Alignment

ORF - retro_ttru_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 55.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PQPLPAERRGLEELEVPVDPLPSSPAQEALDLLFNCGSTEEASSSPG-RGPLTEAELALFDPFSKEEGVG
          PQ...A.R.G...........P...........FNCGST.EAS..P..R.P.T..ELAL.DP.SKEE..G
Retrocopy PQKGGAWRGGASTCWTCQRTIPHATPSPSRPAIFNCGSTKEASRAPA<RAPHTKTELALLDPLSKEEVSG

Parental  PSPTHMGELAALEAESERLDQEPWEPGG-QAEEEDEEGGPAPAYLSEATELITQ-ALRDEKAGAYPAALQ
          .SPT...EL.............P....G.Q.EE...EGGP....LS.ATELITQ..LR.EKA..YPAALQ
Retrocopy LSPTCISELVLMQS-PQGCTRDPGKQEG<QGEE--KEGGPTTTFLSQATELITQ<GLREEKASTYPAALQ

Parental  GYRDGVHILLQGVSGDPSPARREGVKKKAAEYLKR-AEEILHLHLSQLPP
          GYRDGVHILLQG...DPSPA.REGV..KAA..LKR..E.ILHL.LS.L.P
Retrocopy GYRDGVHILLQGDPSDPSPALREGV-RKAAN*LKR<SEAILHLYLS*LLP

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_378 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_378 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000007902	1 retrocopy	retro_pvam_942,
Tursiops truncatus	ENSTTRG00000000324	1 retrocopy	retro_ttru_378 ,