RetrogeneDB ID: retro_ttru_903

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_559:311994..312600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSTTRG00000007019
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_ttru_903
ATGGTGTTGGAAAGCACTATGGTTTGCGTGGACAACAGTGAGTATATGCGGAATGGGGACTTCTTACCCACCCGGCTACA
CGCCCAACAAGACGCTGTCAACATAGTCTGTCACTCCAAGATCCTCAGCAACCCTGAGAACAATGTGGGCCTCATCACAC
TGGCCAATGACTGTGAAGTGCGGACCACACTCACCCCTGACACCGGTCACATCCTGTCTAAGCTCCACACTGTCCAACCG
AAGGGCAAGATCACCTTCTGCACTGGCATCTGCGTGGCCCATCTGGCCCTGAAGCACCAACAGGTCAAGAATCACAAGAT
ACGAATCATTGCCTTTGTGGGAAGCCCCATGGAGGACAATGAGAAGAATCTGGTGAAACTGGCTAAACGCCTCAAGAAGG
AGAAAGTAAATGCTGACATTATCAATTTGGGAGAAGAGGAGGTGAGCACAGAAAAGCTGACCGCCTTTGTAAACACACTG
AATGGCAAAGATGGAAGCGGTTCTCATCCGGTGACAGTGCGTCCTGGGCCCAGCTTGGCCGATGCCCTCATCAGTTCTCC
GATTCTGGCTGGGGAAGGCAGTGCCATGCTGGGTCTTGGTGCCAGT

Alignment

ORF - retro_ttru_903 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.09 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEVLTTLTPDTGR
          MVLESTMVCVDNSEYMRNGDFLPTRL.AQQDAVNIVCHSK..SNPENNVGLITLANDCEV.TTLTPDTG.
Retrocopy MVLESTMVCVDNSEYMRNGDFLPTRLHAQQDAVNIVCHSKILSNPENNVGLITLANDCEVRTTLTPDTGH

Parental  ILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDI
          ILSKLHTVQPKGKITFCTGI.VAHLALKH.Q.KNHK.RIIAFVGSP.EDNEK.LVKLAKRLKKEKVN.DI
Retrocopy ILSKLHTVQPKGKITFCTGICVAHLALKHQQVKNHKIRIIAFVGSPMEDNEKNLVKLAKRLKKEKVNADI

Parental  INFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLADALISSPILAGEGGAMLGLGAS
          IN.GEEEV.TEKLTAFVNTLNGKDG.GSH.VTV.PGPSLADALISSPILAGEG.AMLGLGAS
Retrocopy INLGEEEVSTEKLTAFVNTLNGKDGSGSHPVTVRPGPSLADALISSPILAGEGSAMLGLGAS

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_903 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_903 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903 ,