RetrogeneDB ID: retro_ttru_1229

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107757:35792..36259(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSTTRG00000005258
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_ttru_1229
ATGGCAGCTACTGTCCTTTGCGCCTGTGTCCACCGACTGCCTGCGGCCTTTGTGCTGCTGCCCAGGCTGCTCATGCTGGC
CATGGCCCAGCCACTCAGCACTACCCTTTTCCCCACGGGGGCCCAGAGGAGGCCTGGGGCTCCACAGTTGGCCTCACTGC
TTGTGCAGTTTCCAGTTGGAGTTACACAGCTGTGCCCCCAGTATAGTGAGGCACTCCTTTGACATTAGAGGGGATCAAGG
ACCCTGTCCTTTACGTCTTGAAACTCTATGACAAGATTGACCCAGAAAGGCTCTCAGTAAATTCCCATTTTATGAAAGAT
CTGGGCTTAGACAGTTTGGACTGAGTGGGGATTATAATGGCCATGGAACATGAATTGGGGTTTGAAATTCTTGATGTAGA
TGCAGAGAAGTTAATGTGCCCACAAGAAATTGTAGATTACATTGCAGATAAGAAGGATGCATATGAA

Alignment

ORF - retro_ttru_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAARVLWVCVRRLPAAFAPLPRLPTLAAARSLCTTLFPAGARARSWAPHPASVLTQVPGGVTPLCRQYSD
          MAA.VL..CV.RLPAAF..LPRL..LA.A..L.TTLFP.GA..R..AP..AS.L.Q.P.GVT.LC.QYS.
Retrocopy MAATVLCACVHRLPAAFVLLPRLLMLAMAQPLSTTLFPTGAQRRPGAPQLASLLVQFPVGVTQLCPQYSE

Parental  A-PPLTLEGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLM
          A..PLTLEGIKD.VLYVLKLYDKIDPE.LSVNSHFMKDLGLDSLD.V.IIMAME.E.GFEI.D.DAEKLM
Retrocopy A<TPLTLEGIKDPVLYVLKLYDKIDPERLSVNSHFMKDLGLDSLD*VGIIMAMEHELGFEILDVDAEKLM

Parental  CPQEIVDYIADKKDVYE
          CPQEIVDYIADKKD.YE
Retrocopy CPQEIVDYIADKKDAYE

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_1229 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1229 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 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mustela putorius furo	ENSMPUG00000012142	2 retrocopies	retro_mputfur_1135, retro_mputfur_466,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Tursiops truncatus	ENSTTRG00000005258	2 retrocopies	retro_ttru_1229 , retro_ttru_989,