RetrogeneDB ID: retro_ttru_1138

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105371:4478..5956(+)
• 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_1138
ATGGCATGGGCTCTGAAGCTGCCTCTGACGGATGAGGTGACTGAATCCCGGCTGTGCAGGACTCTGGTGCTAGATTATCC
GGGATCGGCCACAACTGCGTGCTGGTGCCTGTAGCATGAGTGATGTCCTAGCATTGCCCATTTTTAAGCAAGAAGAGTCA
AGTTTGCCTCCAGACAATGAGAATAAAATCCTCCCTTTTCAATATGTGCTTTGTGCTGCCACCTCTCCAGCAGTGAAACT
CCATGATGAACCCTGACATATCTCAATCAAGGCCAGTCTTATGAAATCCGAATACTAGACAACAGGAAACTTGGAGAACT
ACCAGAAATTAATGGCAAATTGGTGAAGAGTGTATTCCATGTTGTGTTCCATGACAGACGGCTACAATACACTGAACATC
AGCAGCTGGAAGGCTGGAGGTGGAACCCACCTGGAGATAGCATTCTTGATATCCCAATGTCTGTGGGTATAATCGATCCT
AGGGCTAATCCAAACCAACTAAATACAGTGGAGTTCCTGTGGGACCCTGCAAGGAGGACATCTGTGTTTATTCAGGTGCA
TTGTATTAGCACAGAGTTCACTATGAGGAAACACGGTGGAGAGAAGGGAGTGCCATTTCGAGTACAAATTGATACCTTCA
TGGAGAATAAGAATGGGGAATATACTGAGCACTTACACTCAGCCAGCTGCCAGATCAAAGTCTTCAAGCCCAAAGGTGCA
GACAGAAAACAAAAAACAGACAGGGAGAAAATGGAGAAACGAACGCCTCATGAGAAGGAGGAGTATCAACCTTCCTATGA
GACAACTATACTCACAGAGTGTTCTCCATGGCCTGAGATCACGTATGTCAATAATTCCCCATCACCTGGCTTCAGCAGTT
CCCATAGCAGTCTTTCTCTTGGGGAAGGAAATGGTTCACCAAATCACCAGCCAGTGGCCCCTCCAGTCACAGATAACCTC
CTGCCAACAACCACACCTCAGGAGGTTCTGCAGTGGTTGCATCGAAACCGTTTTTCCACATTCACGAGGCTTTTTACAAA
CTTTTCAGGGGCAGATTTGTTGAAACTAACTAGAGATGATGTGATTCAAATCTGTGGCCCTGCAGATGGAATCAGACTTT
TTAATGCATTAAAAGGCCTGATGTGAGCCCAAGTCTAACCATTTATGTTTGTCAGGAACCCTTGAAGCTGGGGGAGCAGC
AACAACAGCAGGAGAAGCATGAGGATGGAGACCCAAATACTTTCTTCGTTTACCATACCATCTACCTAGAAGAACTGACA
GATGTTGAACTGACAGAAAAAAATTGCTCAGCTTTTCAGCGTTTCCCCTTGGCAGATCAGCCAGGTCCACAAGCAGGGGC
CCACAGGAATCCGTGTGCTCATTAGTGATGAGATGATACAGAGCTTTCAGGAAGAAGCCTGTTTTATTCTGGACACAATG
AAAGCAGAAACAATGATAGCTATCATATCGTACTGAAG

Alignment

ORF - retro_ttru_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAWALKLPLADEVIESGL-VQDFDASLSGIGQ-ELGAGAYSMSDVLALPIFKQEESSLPPDNENKILPFQ
          MAWALKLPL.DEV.ES.L.VQD..A.LSGIG...L.AGA.SMSDVLALPIFKQEESSLPPDNENKILPFQ
Retrocopy MAWALKLPLTDEVTESRL<VQDSGARLSGIGH<QLRAGACSMSDVLALPIFKQEESSLPPDNENKILPFQ

Parental  YVLCAATSPAVKLHDE-TLTYLNQGQSYEIRMLDNRKLGELPEINGKLVKSIFRVVFHDRRLQYTEHQQL
          YVLCAATSPAVKLHDE.TLTYLNQGQSYEIR.LDNRKLGELPEINGKLVKS.F.VVFHDRRLQYTEHQQL
Retrocopy YVLCAATSPAVKLHDE<TLTYLNQGQSYEIRILDNRKLGELPEINGKLVKSVFHVVFHDRRLQYTEHQQL

Parental  EGWRWNRPGDRILDIDIPMSVGIIDPRANPNQLNTVEFLWDPAKRTSVFIQVHCISTEFTMRKHGGEKGV
          EGWRWN.PGD.ILDI..PMSVGIIDPRANPNQLNTVEFLWDPA.RTSVFIQVHCISTEFTMRKHGGEKGV
Retrocopy EGWRWNPPGDSILDI--PMSVGIIDPRANPNQLNTVEFLWDPARRTSVFIQVHCISTEFTMRKHGGEKGV

Parental  PFRVQIDTFKENENGEYTEHLHSASCQIKVFKPKGADRKQKTDREKMEKRT-HEKEKY--SYETTILTEC
          PFRVQIDTF.EN.NGEYTEHLHSASCQIKVFKPKGADRKQKTDREKMEKRT.HEKE.Y..SYETTILTEC
Retrocopy PFRVQIDTFMENKNGEYTEHLHSASCQIKVFKPKGADRKQKTDREKMEKRTPHEKEEYQPSYETTILTEC

Parental  SPWPEITYVNNSPSPGFNSSHNSFSLGEGNGSPNHQPEPPPPVTDNLLPTTTPQEAQQWLHRN-FSTFTR
          SPWPEITYVNNSPSPGF.SSH.S.SLGEGNGSPNHQP...PPVTDNLLPTTTPQE..QWLHRN.FSTFTR
Retrocopy SPWPEITYVNNSPSPGFSSSHSSLSLGEGNGSPNHQP-VAPPVTDNLLPTTTPQEVLQWLHRNRFSTFTR

Parental  L-TNFSGADLLKLTRDDVIQICGPADGIRLFNALKGRM-VRPRLTIYVCQESLQLREQQQQQQQQQQKHE
          L.TNFSGADLLKLTRDDVIQICGPADGIRLFNALKG.M.V.P.LTIYVCQE.L.L.EQQQQQ.....KHE
Retrocopy LFTNFSGADLLKLTRDDVIQICGPADGIRLFNALKGLM<VSPSLTIYVCQEPLKLGEQQQQQE----KHE

Parental  DGDSNGTFFVYHAIYLEELTAVELTE-KIAQLFSISPCQISQIYKQGPTGIHVLISDEMIQNFQEEACFI
          DGD.N.TFFVYH.IYLEELT.VELTE.KIAQLFS.SP.QISQ..KQGPTGI.VLISDEMIQ.FQEEACFI
Retrocopy DGDPN-TFFVYHTIYLEELTDVELTE>KIAQLFSVSPWQISQVHKQGPTGIRVLISDEMIQSFQEEACFI

Parental  LDTMKAET-NDSYHIILK
          LDTMKAET.NDSYHI.LK
Retrocopy LDTMKAET<NDSYHIVLK

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_1138 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1138 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,