RetrogeneDB ID: retro_ttru_1896

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97697:136945..137561(+)
• 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_1896
CTTGGCTTCCAGCTCAGCCCGGCCGGCTATGCCTTTTCCTGCCCGTGACACCAACCGGAACTTACAAGCAACAGTTGGCG
CCTATTACGACTAAGAGAGGCCAAACCTCAGTGTGCCTTCTGTGTCCTTTGTTGAAGGTGTCATCATAGGAGAAGGGGAG
TCGATACCTCCTGATACTCAGTTTATAAAAACATGGTGGATGCAGAATTCTGGGGCAGAGGCCTGGCCTCCAGGAGTTTG
TTTTAAATACGTCAGAGGAGACCAATTTGGACTTGTGCACGTGGTGATGGGGAGATCTCTAGAGCCCCAAGAGGTCGCAA
ATGTCAACGTCCAGGTGTGCAGCCCGGGCAGAGCAGGAATGTGTCAGGACAGCGGCGGATATGTGCGGCCACAGGACTCT
ACCATGGAGATGTCGTAGGGGTCCTTCTCGGTGTGGAGGTGGGTGGACTTTTAGGAGTAACGCAGCAGCTGTCATCTTTT
GAAACGGAGTGCGACACACAGCCACATCGCAAGGTAGAAGGAAACTTCAACTCCTTTGCCTCTCCCCAAAAGAACCGACA
ATCAGGTGAAACAATTTAAAAGACCCTGGGGATTCCGGTTCGACTCCATCAGCAAA

Alignment

ORF - retro_ttru_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LGFQLNPAGCA-FFLDMTNWNLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQN
          LGFQL.PAG.A.F....TN.NLQA..GAYYD.E.PN.SVPS.SFVE.V.IGEGESIPPDTQFIKTW..QN
Retrocopy LGFQLSPAGYA>FPARDTNRNLQATVGAYYD*ERPNLSVPSVSFVEGVIIGEGESIPPDTQFIKTWWMQN

Parental  SGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQ-GQWRMCTATGLYYGDV
          SGAEAWPPGVC.KYV.GDQFG.V..VM.RSLEPQE.A.V.VQ.CSP.RAGM.Q.GQ.R.C.ATGLY.GDV
Retrocopy SGAEAWPPGVCFKYVRGDQFGLVHVVMGRSLEPQEVANVNVQVCSPGRAGMCQ<GQRRICAATGLYHGDV

Parental  IWVILSVEVGGLLGVTQQLSSFETEFNTQPHRKVEGNFNPFASPQKNRQSDE-NNLKDPG-GSEFDSISK
          ..V.L.VEVGGLLGVTQQLSSFETE..TQPHRKVEGNFN.FASPQKNRQS.E.NNLKDPG.G..FDSISK
Retrocopy VGVLLGVEVGGLLGVTQQLSSFETECDTQPHRKVEGNFNSFASPQKNRQSGE<NNLKDPG<GFRFDSISK

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_1896 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1896 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,