RetrogeneDB ID: retro_ttru_560

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2680:172098..172687(-)
• Located in intron of: None

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_560
TCTTGTGCTGAGTATTCTTTTCATGTGCCAAGTCTAGAGGAGCTTGTTGGAGTTCTGCGGAAGGGGCTAACGGATAACTT
TGCTGATGTCCAGGTCTCTGTAGTTGATTGCCCTAATTTGACCAAGGAGCCATTTACCTTTCCCGTAAAAGGTATCTGTG
GGAAAACTAGAATTGCAGAAGTAGGAGGTGTGCCTTACTTATTGCCTCTTATAAATAAAAAAAAAAGTTTATGATCTAAA
TAAAATCACAAAAGAAATCCAGCTTCCTGGAGCTTTTGTTCTTGGAGCAGGAGCAGGCCCATTTCCGACTCTTGGATTCA
ATTCTGAGTTTATGCCAGTTGTTCAAACAAAAAGTGAACACAAACCTCCTGTGAATGGAAGTTACTTTGCTCATGTTAAC
TCTGCAGATGGAGGGTGCCTACTGGAGAAATACAGTGAGAAATATCATGATTTGGGGTTTGCATTACTGGCTAATCTTTT
TGCCAGTGAAGGACAACCTGGAAAGGTCATTGAGGTGAAATCCAAAAGAAGACCTGGAAAACTTAACTTTGTGACTTGTA
TGAGACAGACTCTTGAAAAACATTATGGA

Alignment

ORF - retro_ttru_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 62.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCAEYSFHVPSLEELVGVLQKGLTDNFADVQVSVVDCPNLTKEPFTFPVKGICGKTRIAEVGGVPYLLPL
          SCAEYSFHVPSLEELVGVL.KGLTDNFADVQVSVVDCPNLTKEPFTFPVKGICGKTRIAEVGGVPYLLPL
Retrocopy SCAEYSFHVPSLEELVGVLRKGLTDNFADVQVSVVDCPNLTKEPFTFPVKGICGKTRIAEVGGVPYLLPL

Parental  TNKKK-VYDLNKIAKEIQLPGAFVLGAGAGPFQTLGFNSEFMPVVQTESEHKPPVNGSYFAHVNSADGGC
          .N....VYDLNKI.KEIQLPGAFVLGAGAGPF.TLGFNSEFMPVVQT.SEHKPPVNGSYFAHVNSADGGC
Retrocopy INXXX>VYDLNKITKEIQLPGAFVLGAGAGPFPTLGFNSEFMPVVQTKSEHKPPVNGSYFAHVNSADGGC

Parental  LLEKYSEKYHDFGFALLANLFASEGQPGKVIEVKAKRRTGKLNFVTCMRQTLEKHYG
          LLEKYSEKYHD.GFALLANLFASEGQPGKVIEVK.KRR.GKLNFVTCMRQTLEKHYG
Retrocopy LLEKYSEKYHDLGFALLANLFASEGQPGKVIEVKSKRRPGKLNFVTCMRQTLEKHYG

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_560 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_560 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 ,