RetrogeneDB ID: retro_ttru_715

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3154:33917..34556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSTTRG00000002117
• Aliases: None
• Description: RNA binding motif, single stranded interacting protein 2 [Source:HGNC Symbol;Acc:9909]

Sequence

>retro_ttru_715
CATCACTTTGGAAAATATATTAAGGCACCTCCTGGTGTACCAGCCTCATCTGATCCCTTGCTTTGCAAATTTGCTGATGG
GGGTCCAAAGAAATGACAGAACCAAGGAAATTTTATGCAAAATGGAAAGCCTGGCCAAGGAATGCAGACATGCGTGGTAT
GGCCTTGACCTATGACCCCACCACAGCTCTTCAGAATGGGTTTTACTCAGCTCCTTATAACATCACCCCCAACAAGATGC
TTGCTCAGTCTGCACTGTCCCCATATCTTCCATCTCCTGTGTCTTCATATCAGAGAGTAACTCAGAAATCTCCTCTTATA
AGTATCTAACCCATCTTGGATGCACTACCAGTCATATCTCATGTAGCCTTCAGGTTCAGTTCTGACACCAGCAATGTATC
ATCCCATTTCTCTCCAGCCTGCCTCCATGATGGGATCTCTTACCCAGCAACTGGGACACCTTTCCCTGAGCAGCAAGGGC
ATATACATGCCAACAGCTGCAGCTATGCAAGGAGCTTACATCTCCCAATACACCCCTGTGCCTTCCTCTTTTTCAGTTGA
GGAGAGTAGCGGCCAGCAAAATCAAGTGACTGTGGATGCTCCCTCAGACCATGGGGTCTATTCTTTCCAGTTCAACAAG

Alignment

ORF - retro_ttru_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 52.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HFNGKYIKTPPGVPAPSDPLLCKFADGGPKKRQNQGKFMQNGR-AWPRNGDMGGMALTYDPTTALQNGFY
          H..GKYIK.PPGVPA.SDPLLCKFADGGPKK.QNQG.FMQNG..AWPRN.DM.GMALTYDPTTALQNGFY
Retrocopy HHFGKYIKAPPGVPASSDPLLCKFADGGPKK*QNQGNFMQNGK<AWPRNADMRGMALTYDPTTALQNGFY

Parental  PAPYNITPNRMLAQSALSPYLPSPVSSYQRVTQTSPLQ-VPNLSWMHHQSYLMQPSGSVLTPGMDHPISL
          .APYNITPN.MLAQSALSPYLPSPVSSYQRVTQ.SPL..V.N.SWMH.QSYLM.PSGSVLTP.M.HPISL
Retrocopy SAPYNITPNKMLAQSALSPYLPSPVSSYQRVTQKSPLI>VSNPSWMHYQSYLM*PSGSVLTPAMYHPISL

Parental  QPASMMGPLTQQLGHLSLSSMGTYMPTAAAMQGAYISQYTPVPSSSVSVEESGSQQNQVTVDAPSDHGVY
          QPASMMG.LTQQLGHLSLSS.G.YMPTAAAMQGAYISQYTPVPSS..SVEES..QQNQVTVDAPSDHGVY
Retrocopy QPASMMGSLTQQLGHLSLSSKGIYMPTAAAMQGAYISQYTPVPSS-FSVEESSGQQNQVTVDAPSDHGVY

Parental  SFQFNK
          SFQFNK
Retrocopy SFQFNK

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_715 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_715 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Myotis lucifugus	ENSMLUG00000000530	1 retrocopy	retro_mluc_1093,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715 ,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,