RetrogeneDB ID: retro_ttru_76

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1142:155227..155796(-)
• Located in intron of: ENSTTRG00000007822

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSTTRG00000003124
• Aliases: None
• Description: lysosomal protein transmembrane 4 beta [Source:HGNC Symbol;Acc:13646]

Sequence

>retro_ttru_76
ATCATCAATGCCGTGGTACTGCTGCTTCTGTTGAGCGCCCTGGCTGATCCAGATCAGTATCACTTTTCAAGTTTTGAACT
CGGAGGTGACTTTGAGTTCATGGATGTTGCCAGCATGTGCACTGCTATTGCAGTTTCTCTTCTCATGATCCTGATCTGTG
CAGTGGCTACTTATGGAGGATACAGGCAACACGTGGCCTGGATCATCCCATTCTCCTGTTACCAGGTCTTTGATTTTTCC
CTGAACACCTTGGTTGCAGTCATTGTGCTTGTTTATCCAGACTCCATCCAGGAATACATACGACAGCTGCCTCCTGATTT
TCTTTACGAAGGTGATAGCATGTCAGTGACTCCTACCTTGTTTGGTCTTTATTATTATTCTGTTTATCAGCATTATCTTT
ACTTTTAAGGGGTACTTGATTAGCTGTGTTTGGAACTGCTACCGATTCATCAGTGGCAGGAACTCCTCCGATGTCCTGGC
CTCTGTTACCAGCAATGACACTACGGTGCTATGCACCCCCATACGACGATGCCGCTGTGAATGGCACCGCCAAGGAGCCG
CCACCACCT

Alignment

ORF - retro_ttru_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IINAVVLLILLSALADPDQYHFSSSELGGDFEFMDDANMCIAIAISLLMILICAMATYGAYKQHAAWIIP
          IINAVVLL.LLSALADPDQYHFSS.ELGGDFEFMD.A.MC.AIA.SLLMILICA.ATYG.Y.QH.AWIIP
Retrocopy IINAVVLLLLLSALADPDQYHFSSFELGGDFEFMDVASMCTAIAVSLLMILICAVATYGGYRQHVAWIIP

Parental  FFCYQIFDFALNTLVAVTVLVYPNSIQEYIRQLPPDFPYKDDIMSVNPT-CLVLIILLFISIILTFKGYL
          F.CYQ.FDF.LNTLVAV.VLVYP.SIQEYIRQLPPDF.Y..D.MSV.PT.CLV.II.LFISII.TFKGYL
Retrocopy FSCYQVFDFSLNTLVAVIVLVYPDSIQEYIRQLPPDFLYEGDSMSVTPT>CLVFIIILFISIIFTFKGYL

Parental  ISCVWNCYRYINGRNSSDVLVYVTSNDTTVL-LPPYDDATVNGAAKEPPPP
          ISCVWNCYR.I.GRNSSDVL..VTSNDTTVL..PPYDDA.VNG.AKEPPPP
Retrocopy ISCVWNCYRFISGRNSSDVLASVTSNDTTVL>APPYDDAAVNGTAKEPPPP

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_76 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_76 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76 ,