RetrogeneDB ID: retro_ttru_1601

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_52203:28..539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf106
• Ensembl ID: ENSTTRG00000007822
• Aliases: None
• Description: chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]

Sequence

>retro_ttru_1601
CTCGGCTTCCAGCTCAACTCGGCCGTCTGCGCCCTCTTCCTGGACATGACCAACTGGAACCTACAAGCAGCAACTGGCGC
CTATTATGACTTTGAGAGCCCAAACATCAGTGAGCCCTCTATGTCCTTTGTTGAAGATGTCACCATAGGAGAAGGGGAGT
TGATACCTCCTGATACTCAATTTATAAAAACATGGCAGATCCAAAATTCTGGGGCAGAGGCCTGGCCTCCAGGGGTTTGT
CTTAAAAAAACCCCTGAAAGACCAATTTGGACATGTGAACATGGTAATGGTGAGATCGCTAGAGCCCCAAGTGATTGCAG
ATGTCAGCGTCCAGATGTGCAACCCCAGCAGAGCAGGAATGTATCAGAACAGTGACAGATGTGCACTGCTACAGGACTCT
ACTATGTAGATGTCATCTGGGTCATTCTCAGTGTGGAGGTGGGTGGACTTTTAGAGTAACACAGCAGCTGTCATCTTTTG
AAACGGAGTTCACACACAGCCACATCACAGG

Alignment

ORF - retro_ttru_1601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 83.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQNS
          LGFQLN.A.CA.FLDMTNWNLQAA.GAYYDFESPNIS.PSMSFVEDVTIGEGE.IPPDTQFIKTW.IQNS
Retrocopy LGFQLNSAVCALFLDMTNWNLQAATGAYYDFESPNISEPSMSFVEDVTIGEGELIPPDTQFIKTWQIQNS

Parental  GAEAWPPGVCL-KYVGGDQFGHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQG-QWRMCTATGLYYGDV
          GAEAWPPGVCL.K....DQFGHVNMVMVRSLEPQ.IADVSVQMC.PSRAGMYQ..Q..MCTATGLYY.DV
Retrocopy GAEAWPPGVCL>KKPLKDQFGHVNMVMVRSLEPQVIADVSVQMCNPSRAGMYQN<Q*QMCTATGLYYVDV

Parental  IWVILSVEVGGLL-GVTQQLSSFETEF-NTQPHRK
          IWVILSVEVGGLL..VTQQLSSFETEF..TQPH..
Retrocopy IWVILSVEVGGLL<RVTQQLSSFETEF<HTQPHHR

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_1601 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1601 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Oryctolagus cuniculus	ENSOCUG00000024862	2 retrocopies	retro_ocun_1955, retro_ocun_499,
Rattus norvegicus	ENSRNOG00000038883	2 retrocopies	retro_rnor_1748, retro_rnor_1749,
Tursiops truncatus	ENSTTRG00000007822	4 retrocopies	retro_ttru_1601 , retro_ttru_1738, retro_ttru_1896, retro_ttru_827,