RetrogeneDB ID: retro_ttru_62

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1097:193336..194744(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFCP2
• Ensembl ID: ENSTTRG00000013836
• Aliases: None
• Description: transcription factor CP2 [Source:HGNC Symbol;Acc:11748]

Sequence

>retro_ttru_62
GGGGCGGGAGAAAAGGTGCGAAAGCGACATGGGAGTGCAGGTGATGTCCAAGCATTGCCCATTTTTAAGCAAGAAGAGTC
AAGTTTGCCTCCAGATAATGAGAATAAAATCCTCCCTTTTCAATATGTGCTTTTTGCTGCCACCTCTCCAGCAGTGAAAC
TCCATGATGAAACCCTGACACATCTCAATCAAGGCCAGTCTTATGAAATCCGAATACTAGACAACAGGAAACTTGGAGAA
CTACCAGAAATTAACGGCAAGTTGGTGAAGAGTGTATTCCGTGTCGTGTTCCATGACAGACGGCTCCAATACACTGAACA
TCAGCAGCTGGAGGGCTGGAGTTGGAACCCACCTGGAGATAGAATTCTTGACGTAGATATCCCAATGTCTGTGGGTATAA
TCGATCCTAGGGCTAATCCAAACCAACTAAATACAGTGGAGTTCCTGTGGGACCCTGCAAAGAGGACATCTGTGTTTATT
CAAGTGCATTGTATTAGCACAGAGTTCACTATGCAGAAACATGGTGGAGAGAAGGGAGTGCCATTTCGAGTACAAACCGA
TACCTTCAAGGAGAATGAGAACGGGGAATATACTGGGCACTTACACTCAGCCAGCTGCCAGATCAAAGTCTTCAAGCCCA
AAGGTGCAGACAGAAAACAAAAAACAGACAGGGGAAAATGGAGAAACGAATGCCTCATGAGAAGGAGAAATAGCAACCTT
CCCATGAGACAACTATACTCACAGGGTGTTCTCCACGGCCCGAGATCATGTATGTCAATAATTCCCCATCACCTGGCTTC
AGCAGTTCCCATAGCAGTCTTTCTCTTGGGGAAGGAAATGGTTCACCAAGTCACCAGCCAGAGCTGCCCCCTCCAGTCAC
AGATAACCTCTTGCCAACAACCACACCTCAGGAGGCTCAGCAGTGATTGCATGGAAACCGTTTTTCCACATTCACGAGGC
TTTTTACAAACGTCTCAGGGGCAGATTTATTGAAACTAACTAGAGATGATGTGATTCAAATCTGTGGCCCTGCAGATGGA
ACCAGACTTTTTAATGCATTAAAAGGCCAGATGGTCGCCCAAGGCTAACCATTTATGTTTGTCAGGAATCCTTGCGGCTG
AGGGGGCAGCGGCAACAGCAGCAGAAGCATGAGGATGGAGACTCAAATGGTACTTTCTTCGTTTACCATGCCATCTACCT
AGAAGAACTGACAGCTGTTGAACCGACAGAAAAAATGGCTCAGCTTTCCAGCATTTCCCCTTGCCAGATCAGCCAGGTCC
ACAAGCAGGGGCCCACAGGAATCCATGTGCTCTTTAGTGATGAGATGATACAGAGCTTTCAGGAAGAAGCCTGTTTTATT
CTGGACACAATGAAAGAAACCAATGATTGCTATCATATTGTACTGAAG

Alignment

ORF - retro_ttru_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIGQELGAGAYSMSDVLALPIFKQEESSLPPDNENKILPFQYVLCAATSPAVKLHDETLTYLNQGQSYEI
          G.G........S..DV.ALPIFKQEESSLPPDNENKILPFQYVL.AATSPAVKLHDETLT.LNQGQSYEI
Retrocopy GAGEKVRKRHGSAGDVQALPIFKQEESSLPPDNENKILPFQYVLFAATSPAVKLHDETLTHLNQGQSYEI

Parental  RMLDNRKLGELPEINGKLVKSIFRVVFHDRRLQYTEHQQLEGWRWNRPGDRILDIDIPMSVGIIDPRANP
          R.LDNRKLGELPEINGKLVKS.FRVVFHDRRLQYTEHQQLEGW.WN.PGDRILD.DIPMSVGIIDPRANP
Retrocopy RILDNRKLGELPEINGKLVKSVFRVVFHDRRLQYTEHQQLEGWSWNPPGDRILDVDIPMSVGIIDPRANP

Parental  NQLNTVEFLWDPAKRTSVFIQVHCISTEFTMRKHGGEKGVPFRVQIDTFKENENGEYTEHLHSASCQIKV
          NQLNTVEFLWDPAKRTSVFIQVHCISTEFTM.KHGGEKGVPFRVQ.DTFKENENGEYT.HLHSASCQIKV
Retrocopy NQLNTVEFLWDPAKRTSVFIQVHCISTEFTMQKHGGEKGVPFRVQTDTFKENENGEYTGHLHSASCQIKV

Parental  FKPKGADRKQKTDR-EKMEKR-THEKEK--YSYETTILTECSPWPEITYVNNSPSPGFNSSHNSFSLGEG
          FKPKGADRKQKTDR..KMEKR..HEKEK...S.ETTILT.CSP.PEI.YVNNSPSPGF.SSH.S.SLGEG
Retrocopy FKPKGADRKQKTDR<GKMEKRMPHEKEK*QPSHETTILTGCSPRPEIMYVNNSPSPGFSSSHSSLSLGEG

Parental  NGSPNHQPEPPPPVTDNLLPTTTPQEAQQWLHRN-FSTFTRL-TNFSGADLLKLTRDDVIQICGPADGIR
          NGSP.HQPE.PPPVTDNLLPTTTPQEAQQ.LH.N.FSTFTRL.TN.SGADLLKLTRDDVIQICGPADG.R
Retrocopy NGSPSHQPELPPPVTDNLLPTTTPQEAQQ*LHGNRFSTFTRLFTNVSGADLLKLTRDDVIQICGPADGTR

Parental  LFNALKGRMV-RPRLTIYVCQESLQLREQQQQQQQQQQKHEDGDSNGTFFVYHAIYLEELTAVELTEKIA
          LFNALKG.MV.RPRLTIYVCQESL.LR.Q.QQQQ....KHEDGDSNGTFFVYHAIYLEELTAVE.TEK.A
Retrocopy LFNALKGQMV<RPRLTIYVCQESLRLRGQRQQQQ----KHEDGDSNGTFFVYHAIYLEELTAVEPTEKMA

Parental  QLFSISPCQISQIYKQGPTGIHVLISDEMIQNFQEEACFILDTMKAETNDSYHIILK
          QL.SISPCQISQ..KQGPTGIHVL.SDEMIQ.FQEEACFILDTMK.ETND.YHI.LK
Retrocopy QLSSISPCQISQVHKQGPTGIHVLFSDEMIQSFQEEACFILDTMK-ETNDCYHIVLK

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_62 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_62 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000000901	1 retrocopy	retro_shar_108,
Tursiops truncatus	ENSTTRG00000013836	2 retrocopies	retro_ttru_1138, retro_ttru_62 ,