RetrogeneDB ID: retro_ttru_11

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3102:76232..77918(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000000752
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NELFCD
• Ensembl ID: ENSTTRG00000008389
• Aliases: None
• Description: negative elongation factor complex member C/D [Source:HGNC Symbol;Acc:15934]

Sequence

>retro_ttru_11
CAGGAGGGGGGCGAGGCACAGGGAGAAGAGGACGCCCAGGTCCAGCAAGAATGCCTGCAGAAATTTTCTACCAGGGATTA
CATCATGGAACCCTCCATCTTTAACACTCTGATGAGGTATTTTCAGGCAGGAGGGTCTCCGGAGGAGGTGATCCGGCTCT
TATCAGACAACTACACAGCTGTGGCCCAGACAGTCAACTTGCTGGCCCAGTGGCTCATTCAGACAGGGGTTGAACCAGTG
CAGGTTCAGCAAACCGTGGAAAACCACTTGAAGACTTTATTGATGAAACAGTTCGACCCCCGCAAAGCAGATTCTATCTT
TACTGAAGAAGGAGAGACCCCCGTTTGGCTTGAACAAATGATTGCACATTCCACGTGGAGAGATCTTGTTTACCAACTGA
CTGAAGCGCACCCAGACTGTTTGATGCTGAACTTCACGGTCAAGCTGATTTCCGATGCAGGATACCACGGGGAGATCACC
GGCGTGGCGGCAGCCTGCCAGCAGTTGGAAGTGTTTTCTAGAGTTCTCTGTACCTCTCTGGCTACACTTTTGGATGGAGG
AGAAGATAACCTTGCAGAAAATCTCCCTCAGTTTGCTAAGATGGTGTGCCACGGGGAGCACACGTACGTGGTGGCCCAGG
TCCTGATGTCCGTGCTGGCCCAGGAAGGGCAGGGGGGTTTGGCCGTGCGCAGGATTGCACAGGAGGTGCAGCGCTTCGCC
CAGGAGAGAGGCCACGATGCCAGTCGGATCTCTCTCGCACTGGGCACAGCTGCCTCCTACCCCCGGCTGTGTCAGGCCCT
TGGGGCGATGTTGTCCAAGGGGGCCCTGAATCCGGCCGACGTCACTGTCCTTTTCAACCTGTTTACCAGCGTGGACCCGC
CTCCAGTTGAACTCATCCGGGTGCCGGCCTTCCTGGACCTCTTCATGGACTCACTCTTTAAACCAGGGGCCAGGATCAAC
CCGGACCACAAGCACAAGTACATCCATATCTTAGCATATGCAGTGAGCGTGGTGGAGACCTGGAAGAAGGACAGGCGTGT
GAGCGTCAATCAAGGCGAGCTGAAGTCAACGGCCAAAGCTGTTGAAACTGTTCACAGTTTGTGTTGCGCTGAGAACAAAG
GGGCTTCTGAACTCGTGGCCGAGCTGAGCACCCTCTATAAGTGTATCAGGTTTCCAGTGGTGGCCATGGGTGTGCTCAAG
TGGGTGCATTGGAGCGTATCAGAGCCGAAGTACTTCCAGCTGCAGACCCACTGCACCCCCGTGCACCTGGCGCTGCTGGA
CCACATCAGCGCCTGCCACCAGCTCCTGCACCCCCAGGTCCTGCAGCTGCTGGTGAAGCTCTTGGAGACGCAGCATTCCC
AGCTGGACGCGATGGAGCAGCTCAAGCTGAAGAAGACTCTCCTGGACAGGCTGGTGCACCTGCTGAGCCAAGGCTACGTA
CTCCCTGTGGTCACTTACATCCGCAGGTGTCTGGAGAAGGGGGACACCGACATTTCCCTCATTCGCTACTTTGTGACCGA
GGTGCTGGATGTGATCGCACCTCCCTACACCTCTGACTTTGTGCAGCTTTTCCTCCCCATCCTGGAAAACGACAGCATCG
CTGGCACCATTAAAATGGAAGGTGAACAGCACCCTGTGACGGAGTTTATAGCTCACTGCCGGTCTCACTTCGTGCTGGTG
GACTGA

Alignment

ORF - retro_ttru_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.46 %
• Parental protein coverage: 64.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMVCHGEHTYLFAQALMSVLAQEEQGGSAVRRAAQEVQRFAQERGHDASQITLALGTAASYPRACQALGA
          KMVCHGEHTY..AQ.LMSVLAQE.QGG.AVRR.AQEVQRFAQERGHDAS.I.LALGTAASYPR.CQALGA
Retrocopy KMVCHGEHTYVVAQVLMSVLAQEGQGGLAVRRIAQEVQRFAQERGHDASRISLALGTAASYPRLCQALGA

Parental  MLSKGALNPADITVLFKMFTSMDPPPVELIRVPAFLDLFMQSLFKPGARINQDHKHKYIHILAYAASVVE
          MLSKGALNPAD.TVLF..FTS.DPPPVELIRVPAFLDLFM.SLFKPGARIN.DHKHKYIHILAYA.SVVE
Retrocopy MLSKGALNPADVTVLFNLFTSVDPPPVELIRVPAFLDLFMDSLFKPGARINPDHKHKYIHILAYAVSVVE

Parental  TWKKNKRVSINKDELKSTSKAVETVHNLCCNENKGASELVAELSTLYQCIRFPVVAMGVLKWVDWTVSEP
          TWKK..RVS.N..ELKST.KAVETVH.LCC.ENKGASELVAELSTLY.CIRFPVVAMGVLKWV.W.VSEP
Retrocopy TWKKDRRVSVNQGELKSTAKAVETVHSLCCAENKGASELVAELSTLYKCIRFPVVAMGVLKWVHWSVSEP

Parental  RYFQLQTDHTPVHLALLDEISTCHQLLHPQVLQLLVKLFETEHSQLDVMEQLELKKTLLDRMVHLLSRGY
          .YFQLQT..TPVHLALLD.IS.CHQLLHPQVLQLLVKL.ET.HSQLD.MEQL.LKKTLLDR.VHLLS.GY
Retrocopy KYFQLQTHCTPVHLALLDHISACHQLLHPQVLQLLVKLLETQHSQLDAMEQLKLKKTLLDRLVHLLSQGY

Parental  VLPVVSYIRKCLEKLDTDISLIRHFVTEVLDVIAPPYTSDFVQLFLPILENDSIAGTIKTEGEHDPVTEF
          VLPVV.YIR.CLEK.DTDISLIR.FVTEVLDVIAPPYTSDFVQLFLPILENDSIAGTIK.EGE..PVTEF
Retrocopy VLPVVTYIRRCLEKGDTDISLIRYFVTEVLDVIAPPYTSDFVQLFLPILENDSIAGTIKMEGEQHPVTEF

Parental  IAHCKSNFILVN
          IAHC.S.F.LV.
Retrocopy IAHCRSHFVLVD

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_11 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_11 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018783	1 retrocopy	retro_btau_1400,
Tursiops truncatus	ENSTTRG00000008389	1 retrocopy	retro_ttru_11 ,