RetrogeneDB ID: retro_ttru_334

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1897:159591..160535(-)
• Located in intron of: ENSTTRG00000002861

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf54
• Ensembl ID: ENSTTRG00000001140
• Aliases: None
• Description: chromosome 11 open reading frame 54 [Source:HGNC Symbol;Acc:30204]

Sequence

>retro_ttru_334
ATGGCTTGCGCTGAGTATTCTTTTCAGCTGTCAAGTCTAGAGGAGCTTGTTGGAGTTCTGCAGAAGGTGCTAAAGGATAA
CTTTGCTGATGTCCAGGTCTCTGTAGTTGAGTGCCCTGATTTGACTAAGGACCATTTACCTTTCCTGTAAAAGGCATCTG
TGGGAAAACTAGAATTGCAGAAGTAGGAGGTATGCCTTACTTATTGCCTCTTGTAAATCAAAAAACAGGTTTATAACCTA
AATAAGATTGCAAAAGAACTCCAACTTCCCAGAGCTTTTATTCTTAGAGCAGGAGTAGACCCATTTCAGACTCTTGGATT
CAATTCTGAGTTTATGTCAGTTGTTCAAACAGAAAGTGAACACAAACCTCCTGTGTATTGAAGTTCATTTGCTCGTATTA
ACCCTAAAGATGGAGGGTGCCTACTAGAGAAGTACAGTGAGAATATCATGATTTGGGGTGTGCATTACTGGCTAATCTTT
TTGCCAGTGGGGGCCAACCTGGAAAGGTCATTGAGATGAAAGCCAAAAGAAGAACTGGAAAACTTAACTTTGTGACTTGT
ATGAGACAGACTCTTGAAAAAGATTATGGAGATAAGCCTGTGGGGCTGGAAGGTACTTTCGTGATTCAGAAGAGAAAAGT
GAAGACTCACATTATGCCCACAGAATTGTCTTCCTGCCCATTGAACTCTGATGAAGACGTGAATAAATTGTTGCATTTTT
ATGAGATGAAGGCTCCTTTGGTCTGTCTGCTGGTTTTTGTCTTCAGAGACCCAGGGTTTGATTTGAGGTTGGAGCACACT
CGGTGTTTCAGTCATCATGGAAAAGGTGGACACTACTATTATGACACCACCCCAGATATAGTGGAATAACTTGGATACTT
CTTACCTGCAGAGTTTCTGTATTGCATTGACCAACCAAAAGAGACCCATTCTTTTGGGCGAGAT

Alignment

ORF - retro_ttru_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSCAEYSFHVPSLEELVGVLQKGLTDNFADVQVSVVDCPNLTKE-PFTFPVKGICGKTRIAEVGGVPYLL
          M.CAEYSF...SLEELVGVLQK.L.DNFADVQVSVV.CP.LTK..PFTFPVKGICGKTRIAEVGG.PYLL
Retrocopy MACAEYSFQLSSLEELVGVLQKVLKDNFADVQVSVVECPDLTKD<PFTFPVKGICGKTRIAEVGGMPYLL

Parental  PLTN-KKKVYDLNKIAKEIQLPGAFVLGAGAGPFQTLGFNSEFMPVVQTESEHKPPVNGSYFAHVNSADG
          PL.N.KK.VY.LNKIAKE.QLP.AF.L.AG..PFQTLGFNSEFM.VVQTESEHKPPV..S.FA..N..DG
Retrocopy PLVN>KKQVYNLNKIAKELQLPRAFILRAGVDPFQTLGFNSEFMSVVQTESEHKPPVY*SSFARINPKDG

Parental  GCLLEKYSE-KYHDFGFALLANLFASEGQPGKVIEVKAKRRTGKLNFVTCMRQTLEKHYGDKPVGMGGTF
          GCLLEKYSE..YHD.G.ALLANLFAS.GQPGKVIE.KAKRRTGKLNFVTCMRQTLEK.YGDKPVG..GTF
Retrocopy GCLLEKYSE<EYHDLGCALLANLFASGGQPGKVIEMKAKRRTGKLNFVTCMRQTLEKDYGDKPVGLEGTF

Parental  VIQKGKVKTHIMPAEY-SCPLNSDEDVNKWLRFYEMKAPLVCLPVFISRDPGFDLRLEHTHCFSHHGEGG
          VIQK.KVKTHIMP.E..SCPLNSDEDVNK.L.FYEMKAPLVCL.VF..RDPGFDLRLEHT.CFSHHG.GG
Retrocopy VIQKRKVKTHIMPTELSSCPLNSDEDVNKLLHFYEMKAPLVCLLVFVFRDPGFDLRLEHTRCFSHHGKGG

Parental  HYHYDTTPDIVEYLGYFLPAEFLYRIDQPTETHSFGRD
          HY.YDTTPDIVE.LGYFLPAEFLY.IDQP.ETHSFGRD
Retrocopy HYYYDTTPDIVE*LGYFLPAEFLYCIDQPKETHSFGRD

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_334 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_334 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013446	1 retrocopy	retro_chof_593,
Cavia porcellus	ENSCPOG00000014146	1 retrocopy	retro_cpor_1286,
Monodelphis domestica	ENSMODG00000000412	2 retrocopies	retro_mdom_1467, retro_mdom_852,
Otolemur garnettii	ENSOGAG00000002523	1 retrocopy	retro_ogar_3359,
Tupaia belangeri	ENSTBEG00000007819	1 retrocopy	retro_tbel_4251,
Tursiops truncatus	ENSTTRG00000001140	3 retrocopies	retro_ttru_244, retro_ttru_334 , retro_ttru_560,