RetrogeneDB ID: retro_ttru_1391

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112142:216323..216994(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSTTRG00000014126
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_ttru_1391
TATGATAGTATTAATGTTATTGATGTAAATAAAGTTGTAGAATATATTCAGAGGCTACAGAAAGAAGATGGTTCTTTTGC
TGGAGTTTTTGGGGAGAAATTGATACAAGATTCTCTTTTTGTGCGGTGGCAACTTTGGCTCTATTGGGGAAGCTGGATGC
TATTAATGTGGAAAAGGCAATCGAATTTGTTTTATCATGTATGAACCTTGATGGTGGATTTGGTTGCAGGTCAGGTTCTG
AATCCCATGCTGGGCAGATCTATTGTTGCACAGGATTCCTGGCTATTACTAGTCAGTTGCATCGACTAAATTCTGATTTA
CTTGGTTGGTGGCTTCATGAATGACAGCTTCCATTAGGTGGACTCAATGGAAGGCCAGAGAAGTTACCAGATGTATGCTA
TTCTTGGTGGGTGTTGGCTTCCCTAAAGATAATTGGAAGGCTTCATTGGATTGACAGAGAGAATCTGCGCTGTTTCATTT
CAGCATGTCAAGATGAAAAAACCGGAGGATTTGCGGACAGGCCAGGAGATATGGTAGTTCCTTTTCATACTCTATTTGGA
ATTGCTGGATTGTCACTTTTGGGAGAAGAACAGATTAAACCTGTTAGCCCTGTTTTTTGCATGCCTGAAGAAATACTTCA
GAGAGTGAACGTTCAGCCTGAACTAGTGAGC

Alignment

ORF - retro_ttru_1391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 67.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDSINVIDVNKVVEYVQSLQKEDGSFAG-DIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMN
          YDSINVIDVNKVVEY.Q.LQKEDGSFAG...WGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMN
Retrocopy YDSINVIDVNKVVEYIQRLQKEDGSFAG<SFWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMN

Parental  FDGGFGCRPGSESHAGQIYCCTGFLAITSQLHRVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVL
          .DGGFGCR.GSESHAGQIYCCTGFLAITSQLHR.NSDLLGWWL.E.QLP.GGLNGRPEKLPDVCYSWWVL
Retrocopy LDGGFGCRSGSESHAGQIYCCTGFLAITSQLHRLNSDLLGWWLHE*QLPLGGLNGRPEKLPDVCYSWWVL

Parental  ASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEHIKPVSP-FCMP
          ASLKIIGRLHWIDRE.LR.FI.ACQDE.TGGFADRPGDMV.PFHTLFGIAGLSLLGEE.IKPVSP.FCMP
Retrocopy ASLKIIGRLHWIDRENLRCFISACQDEKTGGFADRPGDMVVPFHTLFGIAGLSLLGEEQIKPVSPVFCMP

Parental  EEILRRVNVQRELVS
          EEIL.RVNVQ.ELVS
Retrocopy EEILQRVNVQPELVS

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_1391 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1391 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391 , retro_ttru_1767, retro_ttru_214,