RetrogeneDB ID: retro_ttru_1340

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110956:70744..71278(-)
• Located in intron of: ENSTTRG00000003681

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRD5A1
• Ensembl ID: ENSTTRG00000012679
• Aliases: None
• Description: steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1) [Source:HGNC Symbol;Acc:11284]

Sequence

>retro_ttru_1340
TGGCCCAACTGCATCCTGCTGGCCATGTTCCTCGTCCACTATGTGCAACGGGCCTTGATTTCCCCCTTTTCAGATCCGAG
GAGGAAAGCCCACACCATTGTACGCCTTTATATTGGCATTCGTGTTCTGCACCTATAACTGGCTACTTGCAGAGTAGATA
CCTGAGCCAGTATGCAGTGTGTGCTGACGACTGGCTCACTGACCCCTGATTTCTAACAGGTTTTGTCGTGTGGTTGACAG
GCATGCTAATAAACATCCACTCAGATCATGGCCTAAGGAACTTCAGGAAACCAGGGGAGACCAGCTATAAAACACTAAGG
AGAGGGCTTGTTTTAGTACATCACTGCAGCCAGCTACTTCCGAGAAGTCGTCCAGTGGTGCGTCTACACCCTCGCCAGCG
GGTCCGTTCAAGGCTGGGCTTTCGCTCTGTTCACCTTCTGTGTCCTGTTCACCAGGGCTCAGCAGCATCACCAGTGGTAC
CATGAGATATTTGAAGATTATCCAAAATTCAGAAAAATGATGATTCTGTTTTTG

Alignment

ORF - retro_ttru_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WPNCILLTMFLVHYAQRALIFPFL-IRGGKPMPLYTFILAFMFCTYN-GYLQSRYLSQYAVYADNWLTDP
          WPNCILL.MFLVHY.QRALI.PF..IRGGKP.PLY.FILAF.FCTYN.GYLQSRYLSQYAV.AD.WLTDP
Retrocopy WPNCILLAMFLVHYVQRALISPFS>IRGGKPTPLYAFILAFVFCTYN>GYLQSRYLSQYAVCADDWLTDP

Parental  RFLTGFVLWLLGLLINIHSDHVLRNLRKPGETGYKIPRGGL-FEYITAANYFGEVVEWCGFALASWSIQG
          .FLTGFV.WL.G.LINIHSDH.LRN.RKPGET.YK..R.GL.F.YITAA.YF.EVV.WC...LAS.S.QG
Retrocopy *FLTGFVVWLTGMLINIHSDHGLRNFRKPGETSYKTLRRGL>F*YITAASYFREVVQWCVYTLASGSVQG

Parental  WAFAVFTFCVLLTRAQQHHQWYHEKFEDYPKFRKIMIPFL
          WAFA.FTFCVL.TRAQQHHQWYHE.FEDYPKFRK.MI.FL
Retrocopy WAFALFTFCVLFTRAQQHHQWYHEIFEDYPKFRKMMILFL

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_1340 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1340 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005509	1 retrocopy	retro_chof_873,
Homo sapiens	ENSG00000145545	1 retrocopy	retro_hsap_4763,
Gorilla gorilla	ENSGGOG00000016593	1 retrocopy	retro_ggor_2967,
Nomascus leucogenys	ENSNLEG00000011414	1 retrocopy	retro_nleu_2347,
Pongo abelii	ENSPPYG00000015333	1 retrocopy	retro_pabe_3708,
Tursiops truncatus	ENSTTRG00000012679	1 retrocopy	retro_ttru_1340 ,