RetrogeneDB ID: retro_ttru_813

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3520:328521..329316(-)
• Located in intron of: ENSTTRG00000016290

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000016693
• Aliases: None
• Description: None

Sequence

>retro_ttru_813
TCTGACAGAGTTGTTCTTATTGGAGGAAAACCTGATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATATCAGA
GTCTCCCATCAAAGGACATGCTCAGCATTATGATCCCAATGTTTACGATGAAACCTATGATTATGGTGGTTTTACAATGA
TATTTGATGACCGCCGTGGACGTCCCGTGGGATTTCCCATGCCGGGAAGAGGTGGTTTGGACAGAATGCCCCCTGGTCGG
GGTGGGTGTCCCATGCCTCCATCCAGAAGGGATTATGATGATATGAGCCCTCGTCGAGGACCTCCTCCACCTCCTCCTGG
ATGAGGGGGCCCGGGTGGTGGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGGAGGAGAGCTAATGG
CCTATGACAGAAGAGGGAGACCTGGAGACTGTTATGATGGTTTGGTTAGTTTCAGTGCTGATGAAATCTGGGACTCTGCA
GTAGATACATGGAGCCCGTCAGAGTGGCAGACGGCTTATGAACCACAGGGTGGCTCTGGATATGATTATTCCTATGCAGG
GGGTCGTGGCTCATACGGTGATCTTGGTGGACCTATTATTACTACACAAGTAACTATTCCCAAAGATCTGGCTGGATCTA
TTATTGGCAAAGGTGGTCAGCAGATTAAACAAATCCATCATGAGTCAGGAGCTTCGATCAAAATTGATGAGCCTTTAGAA
GGGTCCGAAGATCGGATTATTACCATTACAGGAACACAGGCCCAGATACAGAATGCTCAGTAGTTGCTGCAGAAC

Alignment

ORF - retro_ttru_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.7 %
• Parental protein coverage: 58.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDRVVLIGGKPDRVVECIKIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGR
          .DRVVLIGGKPDRVVECIKIILDLISESPIKG.AQ.YDPN.YDETYDYGGFTM.FDDRRGRPVGFPM.GR
Retrocopy SDRVVLIGGKPDRVVECIKIILDLISESPIKGHAQHYDPNVYDETYDYGGFTMIFDDRRGRPVGFPMPGR

Parental  GGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGR
          GG.DRMPPGRGG.PMPPSRRDYDDMSPRRGPPPPPPG.GG.GG.RARNLPLPPPPPPRGG.LMAYDRRGR
Retrocopy GGLDRMPPGRGGCPMPPSRRDYDDMSPRRGPPPPPPG*GGPGGGRARNLPLPPPPPPRGGELMAYDRRGR

Parental  PGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDL
          PGD.YDG.V.FSADE.WDSA.DTWSPSEWQ.AYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDL
Retrocopy PGDCYDGLVSFSADEIWDSAVDTWSPSEWQTAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDL

Parental  AGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN
          AGSIIGKGGQ.IKQI.HESGASIKIDEPLEGSEDRIITITGTQ.QIQNAQ.LLQN
Retrocopy AGSIIGKGGQQIKQIHHESGASIKIDEPLEGSEDRIITITGTQAQIQNAQ*LLQN

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_813 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_813 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 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023, retro_chof_1589,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813 , retro_ttru_930, retro_ttru_937,