RetrogeneDB ID: retro_ttru_1531

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115416:115987..116279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG4
• Ensembl ID: ENSTTRG00000006146
• Aliases: None
• Description: proteasome (prosome, macropain) assembly chaperone 4 [Source:HGNC Symbol;Acc:21108]

Sequence

>retro_ttru_1531
CATCTAAAGATGCTGCGGCTGACGCACACGCCCTTCCTGTGGGTGGGTAACACGCCACACCTGCGCAACCTTGCCATGGT
CATGTGCACCCGCTACGACCCCATCCCCGTGTCCACAGCCCTCCTCGGAGGCACGTCTGACACGACGTCCACCGGCCTCA
CCCAGCGCTTAGCCAGGAAGACCAGCAAGCAGGTGTTTGTCAGCTATAGCCTTCCAAACACCGACAAGCAGCTTCGCGTC
ACTGGTAGAAAACAGGATCAAGGACGAAATGGAGGCTTTTCCGGAGAAGTTC

Alignment

ORF - retro_ttru_1531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 71.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HFHVMRLTDSLFLWVGATPHLRNLSVAMCTRYDPIPVSTALLGDMSDTTSTGLAQRLARKTSKQVFVSYN
          H....RLT...FLWVG.TPHLRNL...MCTRYDPIPVSTALLG..SDTTSTGL.QRLARKTSKQVFVSY.
Retrocopy HLKMLRLTHTPFLWVGNTPHLRNLAMVMCTRYDPIPVSTALLGGTSDTTSTGLTQRLARKTSKQVFVSYS

Parental  LPNTD-SSFTLLVENRIKEEMEAFPEKF
          LPNTD.SSF..LVENRIK.EMEAFPEKF
Retrocopy LPNTD>SSFASLVENRIKDEMEAFPEKF

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_1531 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1531 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014430	1 retrocopy	retro_amel_1196,
Bos taurus	ENSBTAG00000031249	1 retrocopy	retro_btau_1040,
Myotis lucifugus	ENSMLUG00000024906	1 retrocopy	retro_mluc_802,
Rattus norvegicus	ENSRNOG00000039265	2 retrocopies	retro_rnor_1442, retro_rnor_766,
Sus scrofa	ENSSSCG00000001005	3 retrocopies	retro_sscr_362, retro_sscr_656, retro_sscr_657,
Tursiops truncatus	ENSTTRG00000006146	2 retrocopies	retro_ttru_1531 , retro_ttru_1849,