RetrogeneDB ID: retro_ttru_532

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2610:849270..849830(+)
• Located in intron of: ENSTTRG00000009825

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD164
• Ensembl ID: ENSTTRG00000004181
• Aliases: None
• Description: CD164 molecule, sialomucin [Source:HGNC Symbol;Acc:1632]

Sequence

>retro_ttru_532
CTGGCAGCGCTCTGCGGGCTGAGCGCGGCTCACACCACCACGGCTCACACCACCACCCTGGCCGCGAGCGCAACTACACT
CGCGGCTTTACCGACTATCGCCAGCACAGCCTCGGCGCCGCCGCCGCCGCTCCCGCCGGGCACCACTCCAGCCCCAGAAA
TCTGTGAGAGCCGCAGCACGGTGTTTCCGGTTTTGATGCTAACGCTACCCGTTTGGGGTCAGAATGCAAAGGTAAAAGCT
ACTGTTCAGATAATCCCACAGTTCGTGATGGCAAGGGGGTGACCAGCACAGAATTCTGTCCTGGGCTCCCTGCCACACCA
CTGCCAACCAATTCTGCAGCGAAAACCACAACTCCGCCTTCCCCGTCTACAGCCTGCACCACGGCTACTACATCAGGTAC
AACGGATACCACTTCAACTCCGGCTTCACAACCTGTGCGCAAGTCTACCTTTGGGGCAGCCAGTTTCGTTGAAGGAACTG
TCCTTGTCTTGGGTGTGCAGGCTGTAATTTTCTTTCTCTATAAATTCCACAAATCGAAAGATCGAAACTACCGCACTCTG

Alignment

ORF - retro_ttru_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 95.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAAGCLASLCVMTAAQNTTLAPNTTAPSVLPTTTTTTAPMPPPTLATVTTPAPEICESRNNC-VSCFDPN
          LAA.C..S...........LA...T....LPT...T.A..PPP.L...TTPAPEICESR....VS.FD..
Retrocopy LAALCGLSXXXXXXXXXXXLAASATTLAALPTIAST-ASAPPPPLPPGTTPAPEICESRSTV<VSGFD--

Parental  AANTTCFWIECKGKSYCSDNSTVSDCKVVNSTEFCTVPTATPLPTNSTAKTTTPPSPSTASTTATTSGTT
          .AN.T....ECKGKSYCSDN.TV.D.K.V.STEFC....ATPLPTNS.AKTTTPPSPSTA.TTATTSGTT
Retrocopy -ANATRLGSECKGKSYCSDNPTVRDGKGVTSTEFCPGLPATPLPTNSAAKTTTPPSPSTACTTATTSGTT

Parental  NTTSAPTTQPARKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKSKERNYHTL
          .TTS.P..QP.RKSTF.AASF..G.VLVLGVQAVIFFLYKF.KSK.RNY.TL
Retrocopy DTTSTPASQPVRKSTFGAASFVEGTVLVLGVQAVIFFLYKFHKSKDRNYRTL

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_532 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_532 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017992	3 retrocopies	retro_btau_477, retro_btau_479, retro_btau_503,
Macaca mulatta	ENSMMUG00000007011	1 retrocopy	retro_mmul_2418,
Otolemur garnettii	ENSOGAG00000015500	2 retrocopies	retro_ogar_2245, retro_ogar_3252,
Tursiops truncatus	ENSTTRG00000004181	2 retrocopies	retro_ttru_436, retro_ttru_532 ,