RetrogeneDB ID: retro_ttru_699

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3110:119236..119986(-)
• Located in intron of: ENSTTRG00000008041

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLD
• Ensembl ID: ENSTTRG00000003989
• Aliases: None
• Description: dihydrolipoamide dehydrogenase [Source:HGNC Symbol;Acc:2898]

Sequence

>retro_ttru_699
AACTTTCAACGCATCCTTCAAAAACAAGGATTTAAATTTAAATTGAATACCAAATTTACTGGTGCTACTAAGAAGTCAGA
TGGAAAAATTGATGTTTCTATTGAAGCTGCTTCTGGTGATAAAGCTGAAGTTATCACTTGTGATGTACTCCTGGTTTGCA
TTGGTTGACGACCCTTTACTAAGAATTTGGGACTAGAGGAGCTTGGAATTGAGCTGGATCCTAGAGGTAGAATTCTAGTA
AATACCAGATTCCAAACTAAAATTCCAAATATCTATGCAATCGGCGATGTGGTTGCTGGTCCAATGCTGGCTCACAAAGC
AGAGGATGAAGGCTTTATCTGTGTAGAAGGGATGGCTGGTGGCGCTGTGCGCATTGACTACAATTGTGTACCATCGGTGA
TTTACACACACCCTGAAGTTGCTTGGGTTGGCAAAGCAGAAGAGCAGTTGAAAGAAGAGGGTATTGAGTACAAAGTTGGG
AAATTCCCATTTGCTGCAAACAGCAGAGCTAAGACAAACGCTGACACAGATGGTATGGTGAAGATACTTGGGCAGAAATC
AACAGACAGAGTATTGGGAGCACATATTCTAGGACCAGGTGCTGGTGAAATGATAAATGGAGCTGCTCTTGCACTGGAAT
ATGGAGCATCCTGTGAAGATATAGCTAGAGTCTGTCATGCACATCCGACCTTATCAGAAGCTTTTAGAGAAGCAAACCTG
CCTGCATCATTTGGCAAATTGATCAACTTT

Alignment

ORF - retro_ttru_699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.8 %
• Parental protein coverage: 50.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFQRILQKQGFKFKLNTKVTGATRKPDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGI
          NFQRILQKQGFKFKLNTK.TGAT.K.DGKIDVSIEAASG.KAEVITCDVLLVCIG.RPFTKNLGLEELGI
Retrocopy NFQRILQKQGFKFKLNTKFTGATKKSDGKIDVSIEAASGDKAEVITCDVLLVCIG*RPFTKNLGLEELGI

Parental  ELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNCVPSVIYTHPEV
          ELDPRGRI.VNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEG.ICVEGMAGGAV.IDYNCVPSVIYTHPEV
Retrocopy ELDPRGRILVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGFICVEGMAGGAVRIDYNCVPSVIYTHPEV

Parental  AWVGKSEEQLKEEGLEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMINEAAL
          AWVGK.EEQLKEEG.EYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMIN.AAL
Retrocopy AWVGKAEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMINGAAL

Parental  ALEYGASCEDIARVCHAHPTLSEAFREANLAASFGKSINF
          ALEYGASCEDIARVCHAHPTLSEAFREANL.ASFGK.INF
Retrocopy ALEYGASCEDIARVCHAHPTLSEAFREANLPASFGKLINF

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_699 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_699 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005312	1 retrocopy	retro_cpor_685,
Monodelphis domestica	ENSMODG00000016316	2 retrocopies	retro_mdom_1455, retro_mdom_448,
Oryctolagus cuniculus	ENSOCUG00000014667	1 retrocopy	retro_ocun_437,
Ictidomys tridecemlineatus	ENSSTOG00000007445	1 retrocopy	retro_itri_1226,
Tursiops truncatus	ENSTTRG00000003989	1 retrocopy	retro_ttru_699 ,