RetrogeneDB ID: retro_ttru_1111

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_103504:37274..37987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSTTRG00000011276
• Aliases: None
• Description: H1 histone family, member O, oocyte-specific [Source:HGNC Symbol;Acc:18463]

Sequence

>retro_ttru_1111
GGCCTCTTCCTCAGGCCCATCAGCTCCAAGGCCAAGGGGGCCACCAGCAGCTTCAAATTAGTTCCCAAGAATAAAAGGAA
AATTCAGCCCAAGAGGACGTCCACCACGACAGCTCCCGGGAGATCCAGTGAGGCTGAGGAGAAGGGCCCCAAGAAAGCAA
GTGAGGCAAAGAAGGACCTTCCCAACCCAGTGAGGTGAAAAGAGGACTCAAGAAGCCAGCAGAGGTGAGGACACCTGCCT
CCAAACCAGGAGTACCTAAGGAGAAGACCCCCAGGAAAGGTAGCCAGACCAAAGACCAAGAGGGAAAATTGGGCCAGGCC
AGAAAGGCCTCCCCACGGCCAGCCAAGGCTACACAGGCCCCTCCCAGTGCCAACGAACCAGGCAGGAAGTCAAAGGTCAA
AGGCAGAAGGAGCCGCTGAGATGCCAAGGCCCACAGGAAAACAAAAGCTGAGAGTCAGAGTTCAAAGCTCACGGTCACCA
AGGGCAAGAATGGAGCTGTTTCCCCACACAAAAGAAGAGGGAAGCCAAGGTCCTTAAAGAGGTCACTGTCCAAGCAGCTG
AGGAGGCCAAGAGTCAAGGCTACTGCTCCTCCTAAGGGCAGTGGGTTCGAGATGATGCTTGCGTCACTGGCCAGGAAGAT
AGAGACCCCCAAGGGCCCAAGAAGGCCTGGCTTGCCCAGCAAGGCCTCACTGTCCAAAGTGCCCAGTAGGAAG

Alignment

ORF - retro_ttru_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.56 %
• Parental protein coverage: 70.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLLVRPVNSKARGATGSFKLVPKDKRKIQPRKTSTMTAPRRPGQAEGKDSKKPTESKKNPPN-PGDVKKG
          GL..RP..SKA.GAT.SFKLVPK.KRKIQP..TST.TAP.R...AE.K..KK..E.KK..PN.P..VK.G
Retrocopy GLFLRPISSKAKGATSSFKLVPKNKRKIQPKRTSTTTAPGRSSEAEEKGPKKASEAKKDLPN<PSEVKRG

Parental  SRKPGEGRTAPPKPGAAK-KAPKKGQQTKDQEARLGEAKKSSQQPDKATKAPPIASGPSGKSEVKGGRSS
          ..KP.E.RT...KPG..K.K.P.KG.QTKDQE..LG.A.K.S..P.KAT.APP.A..P..KS.VK.GR.S
Retrocopy LKKPAEVRTPASKPGVPKEKTPRKGSQTKDQEGKLGQARKASPRPAKATQAPPSANEPGRKSKVK-GRRS

Parental  RADTKAHRKTKPGSQSSKPTVTKGEDAAASPAK-KKMGSKVPKKAAAQGAGE-GPKAKAPVPPKGSGSK-
          R.D.KAHRKTK..SQSSK.TVTKG...A.SP.K.KK...KV.K....Q.A.E.G............GS..
Retrocopy R*DAKAHRKTKAESQSSKLTVTKGKNGAVSPHK<KKREAKVLKEVTVQAAEE<GQESRLLLLLRAVGSR<

Parental  MEPVPLARKAEAPKGPRKPGIPTKSSASKAASKK
          M....LARK.E.PKGPR.PG.P.K.S.SK..S.K
Retrocopy MMLASLARKIETPKGPRRPGLPSKASLSKVPSRK

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_1111 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1111 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111 ,