RetrogeneDB ID: retro_ttru_1738

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_89369:178603..179216(-)
• 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_1738
CTCGGCTTCCAGCTCAACCCGGCCGGCTGTGCTTTCCTCCTGGACATGACCAGCTGGAACCTACAAGGAGCAATTGGCGC
CTATTATGACTTTGAGAGCCCAAACATCAGTGTGCCGTCTGTGTCCTTTGTTGAAGATGTCACCATAGGAGAACGGGAGT
CGATATCCCCTTATGCTCAATATATAAAAACATGGCGCATCCAAAATTCTGGGGCAGAGGCCTGGCCTCCAGGGGTTTGT
CTTAAATATGTCAGGGGAGACCAACTTGGACATGTGAACATGGTGTTGGTGAGATTGCTAAACCCCCAGGAGATTGCAGA
TGTCAGCGTCCAGATGTGCAGCCCCAGCAGAGCAGGAATGGATCAGGGACAGTGGCGGATGTGCACTGCTACAGGACTCT
ACTATGGAGATGTCATCTGGGTCATTCTCAGTGTGGAGGCGGGTGGACTTCTAGGAGTAGCACAGCAGCTGTCATCTTTT
GAAACGGAGTTCCACACACAGCCACATCGCAAGGTAGAAGGAAACTTCACCCTGTTTGCCTCTCCCCGAAAGAACCGACA
GTCAGATGAAAACAAAAGACCCTGGGCGTTCCGGGTTCCACTCAATCAGCAAA

Alignment

ORF - retro_ttru_1738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQNS
          LGFQLNPAGCAF.LDMT.WNLQ.AIGAYYDFESPNISVPS.SFVEDVTIGE.ESI.P..Q.IKTWRIQNS
Retrocopy LGFQLNPAGCAFLLDMTSWNLQGAIGAYYDFESPNISVPSVSFVEDVTIGERESISPYAQYIKTWRIQNS

Parental  GAEAWPPGVCLKYVGGDQFGHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIW
          GAEAWPPGVCLKYV.GDQ.GHVNMV.VR.L.PQEIADVSVQMCSPSRAGM.QGQWRMCTATGLYYGDVIW
Retrocopy GAEAWPPGVCLKYVRGDQLGHVNMVLVRLLNPQEIADVSVQMCSPSRAGMDQGQWRMCTATGLYYGDVIW

Parental  VILSVEVGGLLGVTQQLSSFETEFNTQPHRKVEGNFNPFASPQKNRQSDENNLKDP-GGSEFDSISK
          VILSVE.GGLLGV.QQLSSFETEF.TQPHRKVEGNF..FASP.KNRQSDEN..K.P.G.S.F.SISK
Retrocopy VILSVEAGGLLGVAQQLSSFETEFHTQPHRKVEGNFTLFASPRKNRQSDEN--KRP>GRSGFHSISK

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_1738 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1738 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,