RetrogeneDB ID: retro_ttru_1174

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_106372:20345..20857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC117
• Ensembl ID: ENSTTRG00000011845
• Aliases: None
• Description: coiled-coil domain containing 117 [Source:HGNC Symbol;Acc:26599]

Sequence

>retro_ttru_1174
GCCCCAAGCAGCCCGGGCGGGAGCGGGGCGCGCCGATGTGTTTCAGTTCACCGCAGTTCACCGTAGAAAGAAACACAAGC
GAGAGGAGGATTGTCCAGTAAGAAAGAAGAGGCTATAACTGAAGTAGAGCTCTGTGCTGGTCCTAATGACTGGATTCTTT
GTGCACATCAGGATATAGAGGGTCATGGAGTAAATCCGTGCACTAGTGGCCTTTCTGCACCTGGCATGTTAGTTGTTATT
TGTGAAGAGAGGAATCAGACAACAGGAGAACCACAGTGTGAAGTTGCCCGAAGGAGGCTTCAGGAAATTGAGGACAGAAT
AACTGATGAAGATGAACTTGAAGCTGACAGAAATATTAACCGTCTTCCCAGGCTTGTCCTTCCTGATACCATGAAAACAG
GTTTGAAGAGGGAATTTGATGAAGTCTTTACAAAGAAAATGATTGAGTCCATGAGCTGTCCTTCAGGGAGCTTGTGCTCT
GGAAGCCTTTCCCTGAACTCCTTTCTGCTAAA

Alignment

ORF - retro_ttru_1174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.88 %
• Parental protein coverage: 61.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASSSPGGSAARGRVSVHHRKKHKREEEEDDCPVRKKR-LTEAGLCAGPNDWILCAHQDIEGHGVNPCTSG
          A.SSPGGS.AR..VSVH.....K...........K....TE..LCAGPNDWILCAHQDIEGHGVNPCTSG
Retrocopy APSSPGGSGARRCVSVHRSSP*KETQARGGLSSKKEEAITEVELCAGPNDWILCAHQDIEGHGVNPCTSG

Parental  LSAPGMLDVICEEMDQTTGEPQCEVARRRLQEIEDRIIDEDEEVEADRNINHLPSLVLSDTMKTGLKREF
          LSAPGML.VICEE..QTTGEPQCEVARRRLQEIEDRI.DED.E.EADRNIN.LP.LVL.DTMKTGLKREF
Retrocopy LSAPGMLVVICEERNQTTGEPQCEVARRRLQEIEDRITDED-ELEADRNINRLPRLVLPDTMKTGLKREF

Parental  DEVFTKKMIESMSRPS-MELVLWKPLPELLSDK
          DEVFTKKMIESMS.PS..ELVLWKP.PELLS.K
Retrocopy DEVFTKKMIESMSCPS<RELVLWKPFPELLSAK

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_1174 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1174 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020088	1 retrocopy	retro_cjac_2465,
Microcebus murinus	ENSMICG00000004228	2 retrocopies	retro_mmur_431, retro_mmur_914,
Macaca mulatta	ENSMMUG00000007214	1 retrocopy	retro_mmul_2580,
Tursiops truncatus	ENSTTRG00000011845	1 retrocopy	retro_ttru_1174 ,